From bb6f2d2e631fd29dd3588cb794197f65c2198383 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Wed, 21 Feb 2024 16:06:50 +0100 Subject: [PATCH 1/7] move maxHits params into separate genes --- .../mixcr/assembler/CloneAssemblerRunnerTest.java | 8 +++----- .../assembler/CloneFactoryParametersTest.java | 14 +++++++------- .../assembler/VJCClonalAlignerParametersTest.java | 12 ++++++------ .../vdjaligners/KGeneAlignmentParametersTest.java | 2 +- .../vdjaligners/VDJCAlignerParametersTest.java | 6 +++--- .../assembler/CloneAssemblerParametersTest.kt | 8 ++++---- 6 files changed, 24 insertions(+), 26 deletions(-) diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java index 7d79fa000..264b12c90 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneAssemblerRunnerTest.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2014-2023, MiLaboratories Inc. All Rights Reserved + * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved * * Before downloading or accessing the software, please read carefully the * License Agreement available at: @@ -92,10 +92,8 @@ private static CloneSet runFullPipeline(String... fastqFiles) throws IOException LinearGapAlignmentScoring scoring = new LinearGapAlignmentScoring<>(NucleotideSequence.ALPHABET, 5, -9, -12); CloneFactoryParameters factoryParameters = new CloneFactoryParameters( - new VJCClonalAlignerParameters(0.8f, - scoring, 5), - new VJCClonalAlignerParameters(0.8f, - scoring, 5), + new VJCClonalAlignerParameters(0.8f, 3, scoring, 5), + new VJCClonalAlignerParameters(0.8f, 3, scoring, 5), null, new DClonalAlignerParameters(0.85f, 30.0f, 3, scoring) ); diff --git a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java index b2031657a..ec743bcd2 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/CloneFactoryParametersTest.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved * * Before downloading or accessing the software, please read carefully the * License Agreement available at: @@ -23,11 +23,11 @@ public class CloneFactoryParametersTest { @Test public void test1() throws Exception { CloneFactoryParameters paramentrs = new CloneFactoryParameters( - new VJCClonalAlignerParameters(0.3f, + new VJCClonalAlignerParameters(0.3f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3), - new VJCClonalAlignerParameters(0.4f, + new VJCClonalAlignerParameters(0.4f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5), - new VJCClonalAlignerParameters(0.2f, + new VJCClonalAlignerParameters(0.2f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 9), new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) ); @@ -44,9 +44,9 @@ public void test1() throws Exception { @Test public void test2() throws Exception { CloneFactoryParameters paramentrs = new CloneFactoryParameters( - new VJCClonalAlignerParameters(0.3f, + new VJCClonalAlignerParameters(0.3f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3), - new VJCClonalAlignerParameters(0.4f, + new VJCClonalAlignerParameters(0.4f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5), null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) ); @@ -59,4 +59,4 @@ null, new DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.ge deser.getVParameters().setRelativeMinScore(0.34f); assertFalse(clone.equals(deser)); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java index b56691108..fd24a18ec 100644 --- a/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParametersTest.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved + * Copyright (c) 2014-2024, MiLaboratories Inc. All Rights Reserved * * Before downloading or accessing the software, please read carefully the * License Agreement available at: @@ -21,7 +21,7 @@ public class VJCClonalAlignerParametersTest { @Test public void test1() throws Exception { - VJCClonalAlignerParameters paramentrs = new VJCClonalAlignerParameters(0.3f, + VJCClonalAlignerParameters paramentrs = new VJCClonalAlignerParameters(0.3f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3); String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); VJCClonalAlignerParameters deser = GlobalObjectMappers.getPretty().readValue(str, VJCClonalAlignerParameters.class); @@ -31,13 +31,13 @@ public void test1() throws Exception { @Test public void test2() throws Exception { - TestUtil.assertJson(new VJCClonalAlignerParameters(0.3f, + TestUtil.assertJson(new VJCClonalAlignerParameters(0.3f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3), true); - TestUtil.assertJson(new VJCClonalAlignerParameters(0.3f, + TestUtil.assertJson(new VJCClonalAlignerParameters(0.3f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), null, 2, 3), true); - TestUtil.assertJson(new VJCClonalAlignerParameters(0.3f, + TestUtil.assertJson(new VJCClonalAlignerParameters(0.3f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 1, 2, 3), true); } -} \ No newline at end of file +} diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java index d9b1ec64d..ddf5106c7 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/KGeneAlignmentParametersTest.java @@ -22,7 +22,7 @@ public class KGeneAlignmentParametersTest { @Test public void test1() throws Exception { - KGeneAlignmentParameters paramentrs = new KGeneAlignmentParameters(GeneFeature.VRegion, 120, 0.84f, 10, + KGeneAlignmentParameters paramentrs = new KGeneAlignmentParameters(GeneFeature.VRegion, 120, 0.84f, 3, 10, new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring()), null, null); diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java index 6b9be8dab..f68147777 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java @@ -28,17 +28,17 @@ public class VDJCAlignerParametersTest { @Test public void test1() throws Exception { VDJCAlignerParameters paramentrs = new VDJCAlignerParameters( - new KGeneAlignmentParameters(GeneFeature.VRegion, 120, 0.87f, 10, + new KGeneAlignmentParameters(GeneFeature.VRegion, 120, 0.87f, 3, 10, new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring()), null, null), new DAlignerParameters(GeneFeature.DRegion, 0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()), - new KGeneAlignmentParameters(GeneFeature.JRegion, 120, 0.87f, 10, + new KGeneAlignmentParameters(GeneFeature.JRegion, 120, 0.87f, 3, 10, new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring()), null, null), - new KGeneAlignmentParameters(GeneFeature.CExon1, 120, 0.87f, 10, + new KGeneAlignmentParameters(GeneFeature.CExon1, 120, 0.87f, 3, 10, new KAlignerParameters(5, false, false, 1.5f, 0.75f, 1.0f, -0.1f, -0.3f, 4, 10, 15, 2, -10, 40.0f, 0.87f, 7, LinearGapAlignmentScoring.getNucleotideBLASTScoring()), null, null), diff --git a/src/test/kotlin/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.kt b/src/test/kotlin/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.kt index 871b45329..abc7f2046 100644 --- a/src/test/kotlin/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.kt +++ b/src/test/kotlin/com/milaboratory/mixcr/assembler/CloneAssemblerParametersTest.kt @@ -27,11 +27,11 @@ class CloneAssemblerParametersTest { fun test1() { val factoryParameters = CloneFactoryParameters( VJCClonalAlignerParameters( - 0.3f, + 0.3f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3 ), VJCClonalAlignerParameters( - 0.4f, + 0.4f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5 ), null, @@ -61,11 +61,11 @@ class CloneAssemblerParametersTest { fun test2() { val factoryParameters = CloneFactoryParameters( VJCClonalAlignerParameters( - 0.3f, + 0.3f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 3 ), VJCClonalAlignerParameters( - 0.4f, + 0.4f, 3, LinearGapAlignmentScoring.getNucleotideBLASTScoring(), 5 ), null, DClonalAlignerParameters(0.85f, 30.0f, 3, AffineGapAlignmentScoring.getNucleotideBLASTScoring()) From e9774cb0465c877653a72a9da7350a7a2cf31d03 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 22 Feb 2024 12:26:03 +0100 Subject: [PATCH 2/7] update version --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 4c85b523b..4e42742c9 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.6.0-66-force-realign-trigger" +val mixcrAlgoVersion = "4.6.0-68-max-hits-params" // may be blank (will be inherited from mixcr-algo) val milibVersion = "" // may be blank (will be inherited from mixcr-algo or milib) From 1990691ef5422794a16c367e95d02f7f00092aaa Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 22 Feb 2024 12:59:47 +0100 Subject: [PATCH 3/7] update version --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 4e42742c9..6692f2fad 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.6.0-68-max-hits-params" +val mixcrAlgoVersion = "4.6.0-69-max-hits-params" // may be blank (will be inherited from mixcr-algo) val milibVersion = "" // may be blank (will be inherited from mixcr-algo or milib) From ca6b59bfcaf2676f1e2cc65a57c51b094d163df6 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 22 Feb 2024 17:14:25 +0100 Subject: [PATCH 4/7] update version --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 6692f2fad..03b8cd386 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.6.0-69-max-hits-params" +val mixcrAlgoVersion = "4.6.0-70-max-hits-params" // may be blank (will be inherited from mixcr-algo) val milibVersion = "" // may be blank (will be inherited from mixcr-algo or milib) From 54327e8ed1baf1efa6b96e3d7ef21c848c96574e Mon Sep 17 00:00:00 2001 From: gnefedev <14794051+gnefedev@users.noreply.github.com> Date: Thu, 22 Feb 2024 16:24:16 +0000 Subject: [PATCH 5/7] regression tests automated change --- regression/presets/analyze/10x-5gex-cdr3.yaml | 10 +++------- regression/presets/analyze/10x-5gex-full-length.yaml | 10 +++------- regression/presets/analyze/10x-sc-5gex.yaml | 10 +++------- regression/presets/analyze/10x-sc-xcr-vdj.yaml | 10 +++------- .../presets/analyze/10x-vdj-bcr-full-length.yaml | 10 +++------- regression/presets/analyze/10x-vdj-bcr.yaml | 10 +++------- .../analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml | 10 +++------- .../presets/analyze/10x-vdj-tcr-full-length.yaml | 10 +++------- .../analyze/10x-vdj-tcr-multi-barcode-test.yaml | 10 +++------- regression/presets/analyze/10x-vdj-tcr-qc-test.yaml | 10 +++------- regression/presets/analyze/10x-vdj-tcr.yaml | 10 +++------- regression/presets/analyze/abhelix-human-bcr-cdr3.yaml | 10 +++------- .../presets/analyze/abhelix-human-bcr-full-length.yaml | 10 +++------- regression/presets/analyze/abhelix-human-rna-xcr.yaml | 10 +++------- regression/presets/analyze/abhelix-human-tcr-cdr3.yaml | 10 +++------- .../presets/analyze/abhelix-human-tcr-full-length.yaml | 10 +++------- .../presets/analyze/ampliseq-tcrb-plus-cdr3.yaml | 9 ++------- .../analyze/ampliseq-tcrb-plus-full-length.yaml | 9 ++------- regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml | 9 ++------- .../presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml | 10 +++------- .../presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml | 10 +++------- .../analyze/bd-rhapsody-human-bcr-full-length.yaml | 10 +++------- .../presets/analyze/bd-rhapsody-human-bcr-v1.yaml | 10 +++------- .../presets/analyze/bd-rhapsody-human-bcr-v2.yaml | 10 +++------- .../analyze/bd-rhapsody-human-tcr-full-length.yaml | 10 +++------- .../presets/analyze/bd-rhapsody-human-tcr-v1.yaml | 10 +++------- .../presets/analyze/bd-rhapsody-human-tcr-v2.yaml | 10 +++------- .../analyze/bd-rhapsody-mouse-bcr-full-length.yaml | 10 +++------- .../presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml | 10 +++------- .../presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml | 10 +++------- .../analyze/bd-rhapsody-mouse-tcr-full-length.yaml | 10 +++------- .../presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml | 10 +++------- .../presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml | 10 +++------- ...d-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml | 10 +++------- .../analyze/bd-sc-xcr-rhapsody-full-length.yaml | 10 +++------- regression/presets/analyze/biomed2-human-bcr-cdr3.yaml | 9 ++------- .../presets/analyze/biomed2-human-bcr-full-length.yaml | 9 ++------- regression/presets/analyze/biomed2-human-rna-igh.yaml | 9 ++------- regression/presets/analyze/biomed2-human-rna-igkl.yaml | 9 ++------- .../presets/analyze/biomed2-human-rna-trbdg.yaml | 9 ++------- .../cellecta-human-dna-xcr-umi-drivermap-air.yaml | 9 ++------- ...ta-human-rna-xcr-full-length-umi-drivermap-air.yaml | 10 +++------- .../cellecta-human-rna-xcr-umi-drivermap-air.yaml | 10 +++------- .../cellecta-mouse-rna-xcr-umi-drivermap-air.yaml | 10 +++------- regression/presets/analyze/exome-seq.yaml | 9 ++------- regression/presets/analyze/flairr-seq-bcr.yaml | 10 +++------- .../presets/analyze/generic-amplicon-with-umi.yaml | 10 +++------- regression/presets/analyze/generic-amplicon.yaml | 10 +++------- .../presets/analyze/generic-bcr-amplicon-umi.yaml | 10 +++------- regression/presets/analyze/generic-bcr-amplicon.yaml | 10 +++------- .../generic-ht-single-cell-amplicon-with-umi.yaml | 10 +++------- .../analyze/generic-ht-single-cell-amplicon.yaml | 10 +++------- .../generic-ht-single-cell-fragmented-with-umi.yaml | 10 +++------- .../analyze/generic-ht-single-cell-fragmented.yaml | 10 +++------- .../generic-lt-single-cell-amplicon-with-umi.yaml | 10 +++------- .../analyze/generic-lt-single-cell-amplicon.yaml | 10 +++------- .../generic-lt-single-cell-fragmented-with-umi.yaml | 10 +++------- .../analyze/generic-lt-single-cell-fragmented.yaml | 10 +++------- regression/presets/analyze/generic-ont-with-umi.yaml | 10 +++------- regression/presets/analyze/generic-ont.yaml | 10 +++------- .../presets/analyze/generic-pacbio-with-umi.yaml | 10 +++------- regression/presets/analyze/generic-pacbio.yaml | 10 +++------- .../analyze/generic-single-cell-gex-with-umi.yaml | 10 +++------- .../presets/analyze/generic-single-cell-gex.yaml | 10 +++------- .../generic-tcr-amplicon-separate-samples-umi.yaml | 10 +++------- .../presets/analyze/generic-tcr-amplicon-umi.yaml | 10 +++------- regression/presets/analyze/generic-tcr-amplicon.yaml | 10 +++------- regression/presets/analyze/han-et-al-2014.yaml | 10 +++------- .../analyze/illumina-human-rna-trb-ampliseq-plus.yaml | 9 ++------- .../analyze/illumina-human-rna-trb-ampliseq-sr.yaml | 9 ++------- .../invivoscribe-human-dna-igh-fr1-lymphotrack.yaml | 9 ++------- .../invivoscribe-human-dna-igh-fr123-lymphotrack.yaml | 9 ++------- .../invivoscribe-human-dna-igh-fr2-lymphotrack.yaml | 9 ++------- .../invivoscribe-human-dna-igh-fr3-lymphotrack.yaml | 9 ++------- ...invivoscribe-human-dna-ighv-leader-lymphotrack.yaml | 9 ++------- .../invivoscribe-human-dna-igk-lymphotrack.yaml | 9 ++------- .../invivoscribe-human-dna-trb-lymphotrack.yaml | 9 ++------- .../invivoscribe-human-dna-trg-lymphotrack.yaml | 9 ++------- .../presets/analyze/irepertoire-human-dna-igh-lr.yaml | 9 ++------- .../presets/analyze/irepertoire-human-dna-igh-sr.yaml | 9 ++------- .../presets/analyze/irepertoire-human-dna-trb-lr.yaml | 9 ++------- .../presets/analyze/irepertoire-human-dna-trb-sr.yaml | 9 ++------- .../analyze/irepertoire-human-dna-xcr-repseq-lr.yaml | 9 ++------- .../analyze/irepertoire-human-dna-xcr-repseq-sr.yaml | 9 ++------- .../presets/analyze/irepertoire-human-rna-bcr-lr.yaml | 10 +++------- .../presets/analyze/irepertoire-human-rna-bcr-sr.yaml | 10 +++------- .../presets/analyze/irepertoire-human-rna-tcr-lr.yaml | 10 +++------- .../presets/analyze/irepertoire-human-rna-tcr-sr.yaml | 10 +++------- .../analyze/irepertoire-human-rna-xcr-repseq-lr.yaml | 10 +++------- .../irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml | 10 +++------- .../irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml | 10 +++------- .../analyze/irepertoire-human-rna-xcr-repseq-plus.yaml | 10 +++------- .../analyze/irepertoire-human-rna-xcr-repseq-sr.yaml | 10 +++------- .../presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml | 10 +++------- .../presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml | 10 +++------- .../presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml | 10 +++------- .../presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml | 10 +++------- .../analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml | 10 +++------- .../irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml | 10 +++------- .../analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml | 10 +++------- .../analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml | 10 +++------- regression/presets/analyze/mikelov-et-al-2021.yaml | 10 +++------- .../analyze/milab-human-bcr-multiplex-cdr3.yaml | 10 +++------- .../analyze/milab-human-bcr-multiplex-full-length.yaml | 10 +++------- .../presets/analyze/milab-human-dna-tcr-multiplex.yaml | 9 ++------- .../analyze/milab-human-dna-xcr-7genes-multiplex.yaml | 9 ++------- .../analyze/milab-human-rna-ig-umi-multiplex.yaml | 10 +++------- .../analyze/milab-human-rna-tcr-umi-multiplex.yaml | 10 +++------- .../presets/analyze/milab-human-rna-tcr-umi-race.yaml | 10 +++------- .../analyze/milab-human-tcr-dna-multiplex-cdr3.yaml | 9 ++------- .../analyze/milab-human-tcr-rna-multiplex-cdr3.yaml | 10 +++------- .../presets/analyze/milab-human-tcr-rna-race-cdr3.yaml | 10 +++------- .../analyze/milab-human-tcr-rna-race-full-length.yaml | 10 +++------- .../presets/analyze/milab-mouse-rna-tcr-umi-race.yaml | 10 +++------- .../presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml | 10 +++------- .../analyze/milab-mouse-tcr-rna-race-full-length.yaml | 10 +++------- .../presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml | 10 +++------- .../presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml | 10 +++------- regression/presets/analyze/nebnext-human-bcr-cdr3.yaml | 10 +++------- .../presets/analyze/nebnext-human-bcr-full-length.yaml | 10 +++------- .../presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml | 10 +++------- .../analyze/nebnext-human-tcr-bcr-full-length.yaml | 10 +++------- regression/presets/analyze/nebnext-human-tcr-cdr3.yaml | 10 +++------- .../presets/analyze/nebnext-human-tcr-full-length.yaml | 10 +++------- regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml | 10 +++------- .../presets/analyze/nebnext-mouse-bcr-full-length.yaml | 10 +++------- .../presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml | 10 +++------- .../analyze/nebnext-mouse-tcr-bcr-full-length.yaml | 10 +++------- regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml | 10 +++------- .../presets/analyze/nebnext-mouse-tcr-full-length.yaml | 10 +++------- .../analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml | 10 +++------- .../analyze/oncomine-human-bcr-ihg-lr-full-length.yaml | 10 +++------- .../analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml | 9 ++------- .../presets/analyze/oncomine-human-igh-fr1-j.yaml | 9 ++------- .../presets/analyze/oncomine-human-igh-fr2-j.yaml | 9 ++------- .../presets/analyze/oncomine-human-igh-fr3-j.yaml | 9 ++------- .../presets/analyze/oncomine-human-igh-leader-j.yaml | 9 ++------- .../analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml | 9 ++------- .../presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml | 10 +++------- .../analyze/oncomine-human-tcrb-lr-full-length.yaml | 10 +++------- .../presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml | 9 ++------- .../presets/analyze/ont-rna-seq-vdj-full-length.yaml | 10 +++------- regression/presets/analyze/ont-rna-seq.yaml | 10 +++------- regression/presets/analyze/parse-bio-vdj-3gex.yaml | 10 +++------- .../analyze/parsebio-sc-3gex-evercode-wt-mega.yaml | 10 +++------- .../analyze/parsebio-sc-3gex-evercode-wt-mini.yaml | 10 +++------- .../presets/analyze/parsebio-sc-3gex-evercode-wt.yaml | 10 +++------- regression/presets/analyze/pereshlop-test.yaml | 10 +++------- .../analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml | 10 +++------- .../analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml | 10 +++------- regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml | 10 +++------- .../presets/analyze/qiaseq-human-tcr-full-length.yaml | 10 +++------- regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml | 10 +++------- .../presets/analyze/qiaseq-mouse-tcr-full-length.yaml | 10 +++------- regression/presets/analyze/rna-seq.yaml | 10 +++------- regression/presets/analyze/seq-well-vdj.yaml | 10 +++------- regression/presets/analyze/seqwell-vdj-cdr3.yaml | 10 +++------- .../analyze/single-cell-as-sample-no-split.yaml | 10 +++------- .../presets/analyze/single-cell-as-sample-split.yaml | 10 +++------- .../presets/analyze/singleron-2.0.1-vdj-cdr3.yaml | 10 +++------- .../analyze/singleron-human-sc-xcr-gexscope-vdj.yaml | 10 +++------- regression/presets/analyze/smart-seq2-vdj.yaml | 10 +++------- .../presets/analyze/smartseq2-vdj-full-length.yaml | 10 +++------- regression/presets/analyze/split-seq-3gex.yaml | 10 +++------- regression/presets/analyze/split-seq-vdj-3gex.yaml | 10 +++------- regression/presets/analyze/takara-human-bcr-cdr3.yaml | 10 +++------- .../presets/analyze/takara-human-bcr-full-length.yaml | 10 +++------- .../analyze/takara-human-rna-bcr-umi-smarter.yaml | 10 +++------- .../analyze/takara-human-rna-bcr-umi-smartseq.yaml | 10 +++------- .../presets/analyze/takara-human-rna-tcr-smarter.yaml | 10 +++------- .../analyze/takara-human-rna-tcr-umi-smarter-v2.yaml | 10 +++------- .../analyze/takara-human-rna-tcr-umi-smartseq.yaml | 10 +++------- .../presets/analyze/takara-human-tcr-V1-cdr3.yaml | 10 +++------- .../analyze/takara-human-tcr-V1-full-length.yaml | 10 +++------- .../presets/analyze/takara-human-tcr-V2-cdr3.yaml | 10 +++------- .../analyze/takara-human-tcr-V2-full-length.yaml | 10 +++------- regression/presets/analyze/takara-mouse-bcr-cdr3.yaml | 10 +++------- .../presets/analyze/takara-mouse-bcr-full-length.yaml | 10 +++------- .../presets/analyze/takara-mouse-rna-bcr-smarter.yaml | 10 +++------- .../presets/analyze/takara-mouse-rna-tcr-smarter.yaml | 10 +++------- .../analyze/takara-mouse-rna-tcr-umi-smarseq.yaml | 10 +++------- regression/presets/analyze/takara-mouse-tcr-cdr3.yaml | 10 +++------- .../presets/analyze/takara-mouse-tcr-full-length.yaml | 10 +++------- .../analyze/takara-sc-human-rna-tcr-smarter.yaml | 10 +++------- regression/presets/analyze/test-airr-long-ig-base.yaml | 10 +++------- regression/presets/analyze/test-generic.yaml | 10 +++------- regression/presets/analyze/test-gf-intersection.yaml | 10 +++------- .../analyze/test-mikelov-et-al-2021-with-contigs.yaml | 10 +++------- .../test-mikelov-et-al-2021-without-contigs.yaml | 10 +++------- regression/presets/analyze/test-subCloningRegions.yaml | 10 +++------- regression/presets/analyze/test-tag-from-header.yaml | 10 +++------- regression/presets/analyze/test-tcr-shotgun.yaml | 10 +++------- ...rmofisher-human-dna-bcr-oncomine-pan-clonality.yaml | 9 ++------- .../thermofisher-human-dna-igh-oncomine-fr1-j.yaml | 9 ++------- .../thermofisher-human-dna-igh-oncomine-fr2-j.yaml | 9 ++------- .../thermofisher-human-dna-igh-oncomine-fr3-j.yaml | 9 ++------- .../thermofisher-human-dna-igh-oncomine-sr.yaml | 9 ++------- ...thermofisher-human-dna-igh-oncomine-v-leader-j.yaml | 9 ++------- ...rmofisher-human-dna-tcr-oncomine-pan-clonality.yaml | 9 ++------- .../thermofisher-human-dna-trb-oncomine-sr.yaml | 9 ++------- .../thermofisher-human-rna-igh-oncomine-lr.yaml | 10 +++------- .../thermofisher-human-rna-igh-oncomine-sr.yaml | 9 ++------- .../thermofisher-human-rna-trb-oncomine-lr.yaml | 10 +++------- .../thermofisher-human-rna-trb-oncomine-sr.yaml | 9 ++------- .../thermofisher-mouse-dna-igh-ampliseq-sr.yaml | 9 ++------- .../thermofisher-mouse-dna-tcb-ampliseq-sr.yaml | 9 ++------- .../thermofisher-mouse-rna-igh-ampliseq-sr.yaml | 9 ++------- .../thermofisher-mouse-rna-tcb-ampliseq-sr.yaml | 9 ++------- .../presets/analyze/umi-guided-consensus-test.yaml | 10 +++------- .../presets/analyze/vergani-et-al-2017-cdr3.yaml | 10 +++------- .../analyze/vergani-et-al-2017-full-length.yaml | 10 +++------- .../schemas/analyzeBundle/parameters/align.schema.yaml | 2 -- .../VDJCAlignerParameters.schema.yaml | 2 -- 213 files changed, 583 insertions(+), 1481 deletions(-) diff --git a/regression/presets/analyze/10x-5gex-cdr3.yaml b/regression/presets/analyze/10x-5gex-cdr3.yaml index 464ea1a55..470543341 100644 --- a/regression/presets/analyze/10x-5gex-cdr3.yaml +++ b/regression/presets/analyze/10x-5gex-cdr3.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -248,18 +250,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-5gex-full-length.yaml b/regression/presets/analyze/10x-5gex-full-length.yaml index c05490728..075d474b9 100644 --- a/regression/presets/analyze/10x-5gex-full-length.yaml +++ b/regression/presets/analyze/10x-5gex-full-length.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -248,18 +250,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-sc-5gex.yaml b/regression/presets/analyze/10x-sc-5gex.yaml index 464ea1a55..470543341 100644 --- a/regression/presets/analyze/10x-sc-5gex.yaml +++ b/regression/presets/analyze/10x-sc-5gex.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -248,18 +250,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-sc-xcr-vdj.yaml b/regression/presets/analyze/10x-sc-xcr-vdj.yaml index d08f6c104..c34cf2126 100644 --- a/regression/presets/analyze/10x-sc-xcr-vdj.yaml +++ b/regression/presets/analyze/10x-sc-xcr-vdj.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -354,18 +356,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml index baecc3981..53099685e 100644 --- a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -354,18 +356,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml index d08f6c104..c34cf2126 100644 --- a/regression/presets/analyze/10x-vdj-bcr.yaml +++ b/regression/presets/analyze/10x-vdj-bcr.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -354,18 +356,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml index 8919507eb..dbac46f6b 100644 --- a/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -354,18 +356,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml index baecc3981..53099685e 100644 --- a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -354,18 +356,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml index c906502d5..963a48dda 100644 --- a/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml @@ -32,6 +32,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -76,6 +77,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -109,6 +111,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -137,7 +140,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -301,18 +303,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml index b6a51053a..25a5bc5fa 100644 --- a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml @@ -40,6 +40,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -84,6 +85,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -117,6 +119,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -145,7 +148,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -356,18 +358,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/10x-vdj-tcr.yaml b/regression/presets/analyze/10x-vdj-tcr.yaml index d08f6c104..c34cf2126 100644 --- a/regression/presets/analyze/10x-vdj-tcr.yaml +++ b/regression/presets/analyze/10x-vdj-tcr.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -354,18 +356,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml index 6a3187c73..cfd1fb16a 100644 --- a/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/abhelix-human-bcr-full-length.yaml b/regression/presets/analyze/abhelix-human-bcr-full-length.yaml index 052274105..911062331 100644 --- a/regression/presets/analyze/abhelix-human-bcr-full-length.yaml +++ b/regression/presets/analyze/abhelix-human-bcr-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/abhelix-human-rna-xcr.yaml b/regression/presets/analyze/abhelix-human-rna-xcr.yaml index 052274105..911062331 100644 --- a/regression/presets/analyze/abhelix-human-rna-xcr.yaml +++ b/regression/presets/analyze/abhelix-human-rna-xcr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml index 6a3187c73..cfd1fb16a 100644 --- a/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/abhelix-human-tcr-full-length.yaml b/regression/presets/analyze/abhelix-human-tcr-full-length.yaml index 052274105..911062331 100644 --- a/regression/presets/analyze/abhelix-human-tcr-full-length.yaml +++ b/regression/presets/analyze/abhelix-human-tcr-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml index 21ccdb30f..ac1dde586 100644 --- a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml index 48ac6649d..16e761180 100644 --- a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml index 48ac6649d..16e761180 100644 --- a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml b/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml index 207a8388d..00f25c741 100644 --- a/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml +++ b/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml @@ -680,6 +680,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -723,6 +724,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -756,6 +758,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -784,7 +787,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -962,18 +964,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml b/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml index 7bd857090..f064740f0 100644 --- a/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml +++ b/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml @@ -685,6 +685,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -728,6 +729,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -761,6 +763,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -789,7 +792,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -967,18 +969,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml index 7159e6f42..a84af4c43 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml @@ -671,6 +671,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -715,6 +716,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -748,6 +750,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -776,7 +779,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -954,18 +956,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml index 207a8388d..00f25c741 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml @@ -680,6 +680,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -723,6 +724,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -756,6 +758,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -784,7 +787,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -962,18 +964,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml index 207a8388d..00f25c741 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml @@ -680,6 +680,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -723,6 +724,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -756,6 +758,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -784,7 +787,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -962,18 +964,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml index 7159e6f42..a84af4c43 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml @@ -671,6 +671,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -715,6 +716,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -748,6 +750,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -776,7 +779,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -954,18 +956,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml index 207a8388d..00f25c741 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml @@ -680,6 +680,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -723,6 +724,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -756,6 +758,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -784,7 +787,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -962,18 +964,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml index 207a8388d..00f25c741 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml @@ -680,6 +680,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -723,6 +724,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -756,6 +758,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -784,7 +787,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -962,18 +964,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml index 7159e6f42..a84af4c43 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml @@ -671,6 +671,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -715,6 +716,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -748,6 +750,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -776,7 +779,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -954,18 +956,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml index 7bd857090..f064740f0 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml @@ -685,6 +685,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -728,6 +729,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -761,6 +763,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -789,7 +792,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -967,18 +969,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml index 7bd857090..f064740f0 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml @@ -685,6 +685,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -728,6 +729,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -761,6 +763,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -789,7 +792,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -967,18 +969,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml index 7159e6f42..a84af4c43 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml @@ -671,6 +671,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -715,6 +716,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -748,6 +750,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -776,7 +779,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -954,18 +956,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml index 7bd857090..f064740f0 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml @@ -685,6 +685,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -728,6 +729,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -761,6 +763,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -789,7 +792,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -967,18 +969,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml index 7bd857090..f064740f0 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml @@ -685,6 +685,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -728,6 +729,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -761,6 +763,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -789,7 +792,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -967,18 +969,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml index c7543778b..bfcc0e263 100644 --- a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml +++ b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml @@ -2399,6 +2399,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -2443,6 +2444,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -2476,6 +2478,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -2504,7 +2507,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -2682,18 +2684,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml index 7159e6f42..a84af4c43 100644 --- a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml +++ b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml @@ -671,6 +671,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -715,6 +716,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -748,6 +750,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -776,7 +779,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -954,18 +956,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml b/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml index 412013068..3ede1007e 100644 --- a/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/biomed2-human-bcr-full-length.yaml b/regression/presets/analyze/biomed2-human-bcr-full-length.yaml index a4fcf04a7..ae254c262 100644 --- a/regression/presets/analyze/biomed2-human-bcr-full-length.yaml +++ b/regression/presets/analyze/biomed2-human-bcr-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/biomed2-human-rna-igh.yaml b/regression/presets/analyze/biomed2-human-rna-igh.yaml index a4fcf04a7..ae254c262 100644 --- a/regression/presets/analyze/biomed2-human-rna-igh.yaml +++ b/regression/presets/analyze/biomed2-human-rna-igh.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/biomed2-human-rna-igkl.yaml b/regression/presets/analyze/biomed2-human-rna-igkl.yaml index fe9179adb..15b09b336 100644 --- a/regression/presets/analyze/biomed2-human-rna-igkl.yaml +++ b/regression/presets/analyze/biomed2-human-rna-igkl.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/biomed2-human-rna-trbdg.yaml b/regression/presets/analyze/biomed2-human-rna-trbdg.yaml index fe9179adb..15b09b336 100644 --- a/regression/presets/analyze/biomed2-human-rna-trbdg.yaml +++ b/regression/presets/analyze/biomed2-human-rna-trbdg.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml index 2f6400cab..6caafce1a 100644 --- a/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml +++ b/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -107,7 +109,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -246,18 +247,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml index 8dddacc90..c2a71119e 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air.yaml index 7a224b56d..ee82d7807 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/cellecta-mouse-rna-xcr-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-mouse-rna-xcr-umi-drivermap-air.yaml index 4695fcc33..0d4ace743 100644 --- a/regression/presets/analyze/cellecta-mouse-rna-xcr-umi-drivermap-air.yaml +++ b/regression/presets/analyze/cellecta-mouse-rna-xcr-umi-drivermap-air.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/exome-seq.yaml b/regression/presets/analyze/exome-seq.yaml index 598de6548..c0a520802 100644 --- a/regression/presets/analyze/exome-seq.yaml +++ b/regression/presets/analyze/exome-seq.yaml @@ -32,6 +32,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -98,7 +100,6 @@ align: includeDScore: true includeCScore: true minSumScore: 200.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: false @@ -178,18 +179,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/flairr-seq-bcr.yaml b/regression/presets/analyze/flairr-seq-bcr.yaml index d12ace31c..92b5eefd8 100644 --- a/regression/presets/analyze/flairr-seq-bcr.yaml +++ b/regression/presets/analyze/flairr-seq-bcr.yaml @@ -31,6 +31,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 14 @@ -74,6 +75,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 10 @@ -107,6 +109,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 11 @@ -135,7 +138,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -274,18 +276,12 @@ assemble: backgroundIndelRate: 0.001 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-amplicon-with-umi.yaml b/regression/presets/analyze/generic-amplicon-with-umi.yaml index b6b9f2906..456b20ffa 100644 --- a/regression/presets/analyze/generic-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-amplicon-with-umi.yaml @@ -35,6 +35,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -78,6 +79,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -111,6 +113,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -139,7 +142,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -278,18 +280,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-amplicon.yaml b/regression/presets/analyze/generic-amplicon.yaml index f5285f3c6..aa84fe9b1 100644 --- a/regression/presets/analyze/generic-amplicon.yaml +++ b/regression/presets/analyze/generic-amplicon.yaml @@ -31,6 +31,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -74,6 +75,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -107,6 +109,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -135,7 +138,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -215,18 +217,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-bcr-amplicon-umi.yaml b/regression/presets/analyze/generic-bcr-amplicon-umi.yaml index b6b9f2906..456b20ffa 100644 --- a/regression/presets/analyze/generic-bcr-amplicon-umi.yaml +++ b/regression/presets/analyze/generic-bcr-amplicon-umi.yaml @@ -35,6 +35,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -78,6 +79,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -111,6 +113,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -139,7 +142,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -278,18 +280,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-bcr-amplicon.yaml b/regression/presets/analyze/generic-bcr-amplicon.yaml index f5285f3c6..aa84fe9b1 100644 --- a/regression/presets/analyze/generic-bcr-amplicon.yaml +++ b/regression/presets/analyze/generic-bcr-amplicon.yaml @@ -31,6 +31,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -74,6 +75,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -107,6 +109,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -135,7 +138,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -215,18 +217,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml b/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml index c2900e38a..044edc64f 100644 --- a/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -81,6 +82,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -114,6 +116,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -142,7 +145,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -321,18 +323,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml b/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml index 96cd29001..042818d66 100644 --- a/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -81,6 +82,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -114,6 +116,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -142,7 +145,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -274,18 +276,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml b/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml index a42557bc0..ac1e7ee4a 100644 --- a/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml @@ -39,6 +39,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -83,6 +84,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -116,6 +118,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -144,7 +147,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -323,18 +325,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml b/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml index 7de714155..1cc545357 100644 --- a/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml @@ -39,6 +39,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -83,6 +84,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -116,6 +118,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -144,7 +147,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -276,18 +278,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml b/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml index 3804f4921..84083f439 100644 --- a/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml @@ -37,6 +37,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -80,6 +81,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -113,6 +115,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -141,7 +144,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -288,18 +290,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml b/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml index 5b442134c..b4e6b2799 100644 --- a/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml @@ -37,6 +37,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -80,6 +81,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -113,6 +115,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -141,7 +144,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -245,18 +247,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-lt-single-cell-fragmented-with-umi.yaml b/regression/presets/analyze/generic-lt-single-cell-fragmented-with-umi.yaml index e68cd7fdf..b3acc864d 100644 --- a/regression/presets/analyze/generic-lt-single-cell-fragmented-with-umi.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-fragmented-with-umi.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -290,18 +292,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml b/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml index 02671eacd..dc7cadbb3 100644 --- a/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -247,18 +249,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-ont-with-umi.yaml b/regression/presets/analyze/generic-ont-with-umi.yaml index f140822ce..f5b82655d 100644 --- a/regression/presets/analyze/generic-ont-with-umi.yaml +++ b/regression/presets/analyze/generic-ont-with-umi.yaml @@ -33,6 +33,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 14 @@ -76,6 +77,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 10 @@ -109,6 +111,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 11 @@ -137,7 +140,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -276,18 +278,12 @@ assemble: backgroundIndelRate: 0.01 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-ont.yaml b/regression/presets/analyze/generic-ont.yaml index de2166869..4b899b755 100644 --- a/regression/presets/analyze/generic-ont.yaml +++ b/regression/presets/analyze/generic-ont.yaml @@ -29,6 +29,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 14 @@ -72,6 +73,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 10 @@ -105,6 +107,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 11 @@ -133,7 +136,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -213,18 +215,12 @@ assemble: backgroundIndelRate: 0.01 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-pacbio-with-umi.yaml b/regression/presets/analyze/generic-pacbio-with-umi.yaml index e8426f816..c400d98f2 100644 --- a/regression/presets/analyze/generic-pacbio-with-umi.yaml +++ b/regression/presets/analyze/generic-pacbio-with-umi.yaml @@ -32,6 +32,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 14 @@ -75,6 +76,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 10 @@ -108,6 +110,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 11 @@ -136,7 +139,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -275,18 +277,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-pacbio.yaml b/regression/presets/analyze/generic-pacbio.yaml index 113e623c0..e59dadce7 100644 --- a/regression/presets/analyze/generic-pacbio.yaml +++ b/regression/presets/analyze/generic-pacbio.yaml @@ -28,6 +28,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 14 @@ -71,6 +72,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 10 @@ -104,6 +106,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 11 @@ -132,7 +135,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -212,18 +214,12 @@ assemble: backgroundIndelRate: 0.001 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml b/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml index 47ba8c100..0dc1b1e2a 100644 --- a/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml +++ b/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml @@ -39,6 +39,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -83,6 +84,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -116,6 +118,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -144,7 +147,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -248,18 +250,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-single-cell-gex.yaml b/regression/presets/analyze/generic-single-cell-gex.yaml index 13d1ad7bb..699d6566d 100644 --- a/regression/presets/analyze/generic-single-cell-gex.yaml +++ b/regression/presets/analyze/generic-single-cell-gex.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -247,18 +249,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml b/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml index b6b9f2906..456b20ffa 100644 --- a/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml @@ -35,6 +35,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -78,6 +79,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -111,6 +113,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -139,7 +142,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -278,18 +280,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-tcr-amplicon-umi.yaml b/regression/presets/analyze/generic-tcr-amplicon-umi.yaml index b6b9f2906..456b20ffa 100644 --- a/regression/presets/analyze/generic-tcr-amplicon-umi.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon-umi.yaml @@ -35,6 +35,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -78,6 +79,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -111,6 +113,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -139,7 +142,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -278,18 +280,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/generic-tcr-amplicon.yaml b/regression/presets/analyze/generic-tcr-amplicon.yaml index f5285f3c6..aa84fe9b1 100644 --- a/regression/presets/analyze/generic-tcr-amplicon.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon.yaml @@ -31,6 +31,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -74,6 +75,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -107,6 +109,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -135,7 +138,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -215,18 +217,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/han-et-al-2014.yaml b/regression/presets/analyze/han-et-al-2014.yaml index a230d69cc..a216094b2 100644 --- a/regression/presets/analyze/han-et-al-2014.yaml +++ b/regression/presets/analyze/han-et-al-2014.yaml @@ -32,6 +32,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -75,6 +76,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -108,6 +110,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -136,7 +139,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -263,18 +265,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml index 21ccdb30f..ac1dde586 100644 --- a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml +++ b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml index 48ac6649d..16e761180 100644 --- a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml +++ b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/invivoscribe-human-dna-igh-fr1-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igh-fr1-lymphotrack.yaml index f25c1af58..1cb18fd8e 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igh-fr1-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igh-fr1-lymphotrack.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/invivoscribe-human-dna-igh-fr123-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igh-fr123-lymphotrack.yaml index f25c1af58..1cb18fd8e 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igh-fr123-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igh-fr123-lymphotrack.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/invivoscribe-human-dna-igh-fr2-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igh-fr2-lymphotrack.yaml index 834a6e7aa..16d321a73 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igh-fr2-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igh-fr2-lymphotrack.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/invivoscribe-human-dna-igh-fr3-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igh-fr3-lymphotrack.yaml index 702dc12c5..76774c652 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igh-fr3-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igh-fr3-lymphotrack.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/invivoscribe-human-dna-ighv-leader-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-ighv-leader-lymphotrack.yaml index 5b306153c..5062c20a2 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-ighv-leader-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-ighv-leader-lymphotrack.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/invivoscribe-human-dna-igk-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igk-lymphotrack.yaml index 702dc12c5..76774c652 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igk-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igk-lymphotrack.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/invivoscribe-human-dna-trb-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-trb-lymphotrack.yaml index 702dc12c5..76774c652 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-trb-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-trb-lymphotrack.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/invivoscribe-human-dna-trg-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-trg-lymphotrack.yaml index 702dc12c5..76774c652 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-trg-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-trg-lymphotrack.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml index fb7da3db8..ffb568d16 100644 --- a/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml index 072653e7e..910be31e5 100644 --- a/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml index fb7da3db8..ffb568d16 100644 --- a/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml index 072653e7e..910be31e5 100644 --- a/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml index fb7da3db8..ffb568d16 100644 --- a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml index 072653e7e..910be31e5 100644 --- a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml index 0551ba018..f0b206a26 100644 --- a/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml index 18ad18480..4d51b455f 100644 --- a/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml index 0551ba018..f0b206a26 100644 --- a/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml index 18ad18480..4d51b455f 100644 --- a/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml index 0551ba018..f0b206a26 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml index d75b3bc77..673f1afc6 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml index 798e3d804..578d1f246 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml index b377a74f9..9d63da307 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml index 18ad18480..4d51b455f 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml index c276ee782..f4e440677 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml index bfe2e255b..d29d0a1f2 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml index c276ee782..f4e440677 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml index bfe2e255b..d29d0a1f2 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml index c276ee782..f4e440677 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml index 48ca7719b..65d0f4447 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml index c276ee782..f4e440677 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml index bfe2e255b..d29d0a1f2 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/mikelov-et-al-2021.yaml b/regression/presets/analyze/mikelov-et-al-2021.yaml index 3169453d8..3f18182ce 100644 --- a/regression/presets/analyze/mikelov-et-al-2021.yaml +++ b/regression/presets/analyze/mikelov-et-al-2021.yaml @@ -56,6 +56,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -99,6 +100,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -132,6 +134,7 @@ align: geneFeatureToAlign: "CBegin(0,15)" minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -160,7 +163,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -299,18 +301,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml index 2e53532c2..73ba07666 100644 --- a/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml b/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml index 9e24995ce..9c07939cd 100644 --- a/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml +++ b/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-dna-tcr-multiplex.yaml b/regression/presets/analyze/milab-human-dna-tcr-multiplex.yaml index 483aec72a..2b38f8900 100644 --- a/regression/presets/analyze/milab-human-dna-tcr-multiplex.yaml +++ b/regression/presets/analyze/milab-human-dna-tcr-multiplex.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-dna-xcr-7genes-multiplex.yaml b/regression/presets/analyze/milab-human-dna-xcr-7genes-multiplex.yaml index 483aec72a..2b38f8900 100644 --- a/regression/presets/analyze/milab-human-dna-xcr-7genes-multiplex.yaml +++ b/regression/presets/analyze/milab-human-dna-xcr-7genes-multiplex.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-rna-ig-umi-multiplex.yaml b/regression/presets/analyze/milab-human-rna-ig-umi-multiplex.yaml index 9e24995ce..9c07939cd 100644 --- a/regression/presets/analyze/milab-human-rna-ig-umi-multiplex.yaml +++ b/regression/presets/analyze/milab-human-rna-ig-umi-multiplex.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-rna-tcr-umi-multiplex.yaml b/regression/presets/analyze/milab-human-rna-tcr-umi-multiplex.yaml index 68d8da422..949966fc7 100644 --- a/regression/presets/analyze/milab-human-rna-tcr-umi-multiplex.yaml +++ b/regression/presets/analyze/milab-human-rna-tcr-umi-multiplex.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-rna-tcr-umi-race.yaml b/regression/presets/analyze/milab-human-rna-tcr-umi-race.yaml index b7ba47474..0ce602bef 100644 --- a/regression/presets/analyze/milab-human-rna-tcr-umi-race.yaml +++ b/regression/presets/analyze/milab-human-rna-tcr-umi-race.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml index 483aec72a..2b38f8900 100644 --- a/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml index 68d8da422..949966fc7 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml index b7ba47474..0ce602bef 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml b/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml index b7ba47474..0ce602bef 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-mouse-rna-tcr-umi-race.yaml b/regression/presets/analyze/milab-mouse-rna-tcr-umi-race.yaml index 62c3971c3..16546b8d2 100644 --- a/regression/presets/analyze/milab-mouse-rna-tcr-umi-race.yaml +++ b/regression/presets/analyze/milab-mouse-rna-tcr-umi-race.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml b/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml index 62c3971c3..16546b8d2 100644 --- a/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml +++ b/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml b/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml index 62c3971c3..16546b8d2 100644 --- a/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml +++ b/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml b/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml index ec7fa6879..33459abc5 100644 --- a/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml +++ b/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml b/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml index fc8efc3d8..c1d074c82 100644 --- a/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml +++ b/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml index 91ab03baf..92348ead8 100644 --- a/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-human-bcr-full-length.yaml b/regression/presets/analyze/nebnext-human-bcr-full-length.yaml index ec7fa6879..33459abc5 100644 --- a/regression/presets/analyze/nebnext-human-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-bcr-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml index 91ab03baf..92348ead8 100644 --- a/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml b/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml index ec7fa6879..33459abc5 100644 --- a/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml index 91ab03baf..92348ead8 100644 --- a/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-human-tcr-full-length.yaml b/regression/presets/analyze/nebnext-human-tcr-full-length.yaml index ec7fa6879..33459abc5 100644 --- a/regression/presets/analyze/nebnext-human-tcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml index 032726a2f..6dacb832a 100644 --- a/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml index fc8efc3d8..c1d074c82 100644 --- a/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml index 032726a2f..6dacb832a 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml index fc8efc3d8..c1d074c82 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml index 032726a2f..6dacb832a 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml index fc8efc3d8..c1d074c82 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml index b6aa143e3..0414d31f2 100644 --- a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml index 4535c7f7d..d86ca095b 100644 --- a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml b/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml index 1686a389d..0724740df 100644 --- a/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml index 6b8229014..7303832b3 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml index d671441fd..b019f7285 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml index 1686a389d..0724740df 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-igh-leader-j.yaml b/regression/presets/analyze/oncomine-human-igh-leader-j.yaml index 92870afc2..265fe2ea7 100644 --- a/regression/presets/analyze/oncomine-human-igh-leader-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-leader-j.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml index 1686a389d..0724740df 100644 --- a/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml index 4444bff1b..96ee004b6 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml index f142aef0c..6d35495e6 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml index 77ae92361..ce0e5b720 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml b/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml index de2166869..4b899b755 100644 --- a/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml +++ b/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml @@ -29,6 +29,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 14 @@ -72,6 +73,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 10 @@ -105,6 +107,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 11 @@ -133,7 +136,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -213,18 +215,12 @@ assemble: backgroundIndelRate: 0.01 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/ont-rna-seq.yaml b/regression/presets/analyze/ont-rna-seq.yaml index de2166869..4b899b755 100644 --- a/regression/presets/analyze/ont-rna-seq.yaml +++ b/regression/presets/analyze/ont-rna-seq.yaml @@ -29,6 +29,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 14 @@ -72,6 +73,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 10 @@ -105,6 +107,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 11 @@ -133,7 +136,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -213,18 +215,12 @@ assemble: backgroundIndelRate: 0.01 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/parse-bio-vdj-3gex.yaml b/regression/presets/analyze/parse-bio-vdj-3gex.yaml index 97e3ef689..a1bd96a95 100644 --- a/regression/presets/analyze/parse-bio-vdj-3gex.yaml +++ b/regression/presets/analyze/parse-bio-vdj-3gex.yaml @@ -847,6 +847,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -891,6 +892,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -924,6 +926,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -952,7 +955,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -1056,18 +1058,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml index 97e3ef689..a1bd96a95 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml @@ -847,6 +847,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -891,6 +892,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -924,6 +926,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -952,7 +955,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -1056,18 +1058,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml index 916eb2efe..1311bee5a 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml @@ -511,6 +511,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -555,6 +556,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -588,6 +590,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -616,7 +619,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -720,18 +722,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml index a42c0100d..58ea9e08a 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml @@ -655,6 +655,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -699,6 +700,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -732,6 +734,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -760,7 +763,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -864,18 +866,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/pereshlop-test.yaml b/regression/presets/analyze/pereshlop-test.yaml index 5ab86b603..3d3978b28 100644 --- a/regression/presets/analyze/pereshlop-test.yaml +++ b/regression/presets/analyze/pereshlop-test.yaml @@ -29,6 +29,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -72,6 +73,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -105,6 +107,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -133,7 +136,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -205,18 +207,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml b/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml index f6855da69..f87122dad 100644 --- a/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml +++ b/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml @@ -45,6 +45,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -88,6 +89,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -121,6 +123,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -149,7 +152,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -288,18 +290,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml b/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml index 6f64240cd..6d38a4eba 100644 --- a/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml +++ b/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml @@ -45,6 +45,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -88,6 +89,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -121,6 +123,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -149,7 +152,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -288,18 +290,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml b/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml index f95d03d89..82cf60ec5 100644 --- a/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml @@ -45,6 +45,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -88,6 +89,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -121,6 +123,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -149,7 +152,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -288,18 +290,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml b/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml index f6855da69..f87122dad 100644 --- a/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml +++ b/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml @@ -45,6 +45,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -88,6 +89,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -121,6 +123,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -149,7 +152,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -288,18 +290,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml index 75a23aa20..06a72aef9 100644 --- a/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml @@ -45,6 +45,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -88,6 +89,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -121,6 +123,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -149,7 +152,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -288,18 +290,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml index 6f64240cd..6d38a4eba 100644 --- a/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml @@ -45,6 +45,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -88,6 +89,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -121,6 +123,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -149,7 +152,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -288,18 +290,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/rna-seq.yaml b/regression/presets/analyze/rna-seq.yaml index 7f099f4f5..e3cfb4b8e 100644 --- a/regression/presets/analyze/rna-seq.yaml +++ b/regression/presets/analyze/rna-seq.yaml @@ -32,6 +32,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -97,6 +99,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -125,7 +128,6 @@ align: includeDScore: true includeCScore: true minSumScore: 200.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: false @@ -205,18 +207,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/seq-well-vdj.yaml b/regression/presets/analyze/seq-well-vdj.yaml index c51adbffc..ab21f751f 100644 --- a/regression/presets/analyze/seq-well-vdj.yaml +++ b/regression/presets/analyze/seq-well-vdj.yaml @@ -35,6 +35,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -78,6 +79,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -111,6 +113,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -139,7 +142,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -318,18 +320,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/seqwell-vdj-cdr3.yaml b/regression/presets/analyze/seqwell-vdj-cdr3.yaml index c51adbffc..ab21f751f 100644 --- a/regression/presets/analyze/seqwell-vdj-cdr3.yaml +++ b/regression/presets/analyze/seqwell-vdj-cdr3.yaml @@ -35,6 +35,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -78,6 +79,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -111,6 +113,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -139,7 +142,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -318,18 +320,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/single-cell-as-sample-no-split.yaml b/regression/presets/analyze/single-cell-as-sample-no-split.yaml index 2a4081608..57c7fe755 100644 --- a/regression/presets/analyze/single-cell-as-sample-no-split.yaml +++ b/regression/presets/analyze/single-cell-as-sample-no-split.yaml @@ -48,6 +48,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -92,6 +93,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -125,6 +127,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -153,7 +156,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -287,18 +289,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/single-cell-as-sample-split.yaml b/regression/presets/analyze/single-cell-as-sample-split.yaml index 374d052b2..a3d3989fd 100644 --- a/regression/presets/analyze/single-cell-as-sample-split.yaml +++ b/regression/presets/analyze/single-cell-as-sample-split.yaml @@ -48,6 +48,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -92,6 +93,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -125,6 +127,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -153,7 +156,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -279,18 +281,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml b/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml index 149821664..7038cf98e 100644 --- a/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml +++ b/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml @@ -35,6 +35,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -78,6 +79,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -111,6 +113,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -139,7 +142,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -289,18 +291,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml b/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml index 149821664..7038cf98e 100644 --- a/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml +++ b/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml @@ -35,6 +35,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -78,6 +79,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -111,6 +113,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -139,7 +142,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -289,18 +291,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/smart-seq2-vdj.yaml b/regression/presets/analyze/smart-seq2-vdj.yaml index 6c2f18335..664146230 100644 --- a/regression/presets/analyze/smart-seq2-vdj.yaml +++ b/regression/presets/analyze/smart-seq2-vdj.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -247,18 +249,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/smartseq2-vdj-full-length.yaml b/regression/presets/analyze/smartseq2-vdj-full-length.yaml index 6c2f18335..664146230 100644 --- a/regression/presets/analyze/smartseq2-vdj-full-length.yaml +++ b/regression/presets/analyze/smartseq2-vdj-full-length.yaml @@ -38,6 +38,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -82,6 +83,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -115,6 +117,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -143,7 +146,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -247,18 +249,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/split-seq-3gex.yaml b/regression/presets/analyze/split-seq-3gex.yaml index 2d2cfb160..3e275b680 100644 --- a/regression/presets/analyze/split-seq-3gex.yaml +++ b/regression/presets/analyze/split-seq-3gex.yaml @@ -653,6 +653,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -697,6 +698,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -730,6 +732,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -758,7 +761,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -862,18 +864,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/split-seq-vdj-3gex.yaml b/regression/presets/analyze/split-seq-vdj-3gex.yaml index 2d2cfb160..3e275b680 100644 --- a/regression/presets/analyze/split-seq-vdj-3gex.yaml +++ b/regression/presets/analyze/split-seq-vdj-3gex.yaml @@ -653,6 +653,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner2 @@ -697,6 +698,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -730,6 +732,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -758,7 +761,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -862,18 +864,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-bcr-cdr3.yaml b/regression/presets/analyze/takara-human-bcr-cdr3.yaml index 1066debdf..0055e2f4e 100644 --- a/regression/presets/analyze/takara-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/takara-human-bcr-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-bcr-full-length.yaml b/regression/presets/analyze/takara-human-bcr-full-length.yaml index e55d6805b..9a672005e 100644 --- a/regression/presets/analyze/takara-human-bcr-full-length.yaml +++ b/regression/presets/analyze/takara-human-bcr-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml b/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml index e55d6805b..9a672005e 100644 --- a/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml +++ b/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml b/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml index e55d6805b..9a672005e 100644 --- a/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml +++ b/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml b/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml index 9b20cee4f..6d203b902 100644 --- a/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml +++ b/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml b/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml index 0296489fb..6e68b7166 100644 --- a/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml +++ b/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml b/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml index 0296489fb..6e68b7166 100644 --- a/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml +++ b/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml b/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml index 55b923f3c..0bbc6ee56 100644 --- a/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml +++ b/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml b/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml index 9b20cee4f..6d203b902 100644 --- a/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml +++ b/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml b/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml index 993731022..f4ae7ce91 100644 --- a/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml +++ b/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml b/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml index 0296489fb..6e68b7166 100644 --- a/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml +++ b/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml b/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml index f88c28c40..e193468ca 100644 --- a/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml +++ b/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-mouse-bcr-full-length.yaml b/regression/presets/analyze/takara-mouse-bcr-full-length.yaml index 94f701acc..1a6222763 100644 --- a/regression/presets/analyze/takara-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/takara-mouse-bcr-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml b/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml index 94f701acc..1a6222763 100644 --- a/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml +++ b/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml b/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml index 94f701acc..1a6222763 100644 --- a/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml +++ b/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-mouse-rna-tcr-umi-smarseq.yaml b/regression/presets/analyze/takara-mouse-rna-tcr-umi-smarseq.yaml index 045c4b450..7caf94601 100644 --- a/regression/presets/analyze/takara-mouse-rna-tcr-umi-smarseq.yaml +++ b/regression/presets/analyze/takara-mouse-rna-tcr-umi-smarseq.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml b/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml index f88c28c40..e193468ca 100644 --- a/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-mouse-tcr-full-length.yaml b/regression/presets/analyze/takara-mouse-tcr-full-length.yaml index 94f701acc..1a6222763 100644 --- a/regression/presets/analyze/takara-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/takara-mouse-tcr-full-length.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/takara-sc-human-rna-tcr-smarter.yaml b/regression/presets/analyze/takara-sc-human-rna-tcr-smarter.yaml index 46b2fa7df..155016f4d 100644 --- a/regression/presets/analyze/takara-sc-human-rna-tcr-smarter.yaml +++ b/regression/presets/analyze/takara-sc-human-rna-tcr-smarter.yaml @@ -60,6 +60,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +104,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -136,6 +138,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -164,7 +167,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -268,18 +270,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/test-airr-long-ig-base.yaml b/regression/presets/analyze/test-airr-long-ig-base.yaml index 081ea17d4..efc7ecfbc 100644 --- a/regression/presets/analyze/test-airr-long-ig-base.yaml +++ b/regression/presets/analyze/test-airr-long-ig-base.yaml @@ -29,6 +29,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -72,6 +73,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -105,6 +107,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -133,7 +136,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: specificMutationProbability: 0.001 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/test-generic.yaml b/regression/presets/analyze/test-generic.yaml index 02920368f..805b1f916 100644 --- a/regression/presets/analyze/test-generic.yaml +++ b/regression/presets/analyze/test-generic.yaml @@ -29,6 +29,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -72,6 +73,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -105,6 +107,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -133,7 +136,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -213,18 +215,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/test-gf-intersection.yaml b/regression/presets/analyze/test-gf-intersection.yaml index 47dd9844e..07b29c123 100644 --- a/regression/presets/analyze/test-gf-intersection.yaml +++ b/regression/presets/analyze/test-gf-intersection.yaml @@ -31,6 +31,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -74,6 +75,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -107,6 +109,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -135,7 +138,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -274,18 +276,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml b/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml index 084531b97..5b537edf3 100644 --- a/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml +++ b/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml @@ -57,6 +57,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -100,6 +101,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -133,6 +135,7 @@ align: geneFeatureToAlign: "CBegin(0,15)" minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -161,7 +164,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -300,18 +302,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml b/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml index 3169453d8..3f18182ce 100644 --- a/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml +++ b/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml @@ -56,6 +56,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -99,6 +100,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -132,6 +134,7 @@ align: geneFeatureToAlign: "CBegin(0,15)" minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -160,7 +163,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -299,18 +301,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/test-subCloningRegions.yaml b/regression/presets/analyze/test-subCloningRegions.yaml index b5b50909b..766b6f7d9 100644 --- a/regression/presets/analyze/test-subCloningRegions.yaml +++ b/regression/presets/analyze/test-subCloningRegions.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -214,18 +216,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/test-tag-from-header.yaml b/regression/presets/analyze/test-tag-from-header.yaml index d73040d29..55dc4f780 100644 --- a/regression/presets/analyze/test-tag-from-header.yaml +++ b/regression/presets/analyze/test-tag-from-header.yaml @@ -31,6 +31,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -74,6 +75,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -107,6 +109,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -135,7 +138,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -215,18 +217,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/test-tcr-shotgun.yaml b/regression/presets/analyze/test-tcr-shotgun.yaml index bd715423b..659c0e249 100644 --- a/regression/presets/analyze/test-tcr-shotgun.yaml +++ b/regression/presets/analyze/test-tcr-shotgun.yaml @@ -31,6 +31,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner @@ -69,6 +70,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -96,6 +98,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -124,7 +127,6 @@ align: includeDScore: true includeCScore: true minSumScore: 200.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: true @@ -204,18 +206,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml b/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml index 1686a389d..0724740df 100644 --- a/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml index 6b8229014..7303832b3 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml index d671441fd..b019f7285 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml index 1686a389d..0724740df 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml index 77ae92361..ce0e5b720 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml index 92870afc2..265fe2ea7 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-dna-tcr-oncomine-pan-clonality.yaml b/regression/presets/analyze/thermofisher-human-dna-tcr-oncomine-pan-clonality.yaml index 1686a389d..0724740df 100644 --- a/regression/presets/analyze/thermofisher-human-dna-tcr-oncomine-pan-clonality.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-tcr-oncomine-pan-clonality.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VGeneWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-dna-trb-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-dna-trb-oncomine-sr.yaml index 77ae92361..ce0e5b720 100644 --- a/regression/presets/analyze/thermofisher-human-dna-trb-oncomine-sr.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-trb-oncomine-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-lr.yaml b/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-lr.yaml index 4535c7f7d..d86ca095b 100644 --- a/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-lr.yaml +++ b/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-sr.yaml index 77ae92361..ce0e5b720 100644 --- a/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-sr.yaml +++ b/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-lr.yaml b/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-lr.yaml index f142aef0c..6d35495e6 100644 --- a/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-lr.yaml +++ b/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-lr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -103,6 +105,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -131,7 +134,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -211,18 +213,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-sr.yaml index 77ae92361..ce0e5b720 100644 --- a/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-sr.yaml +++ b/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-mouse-dna-igh-ampliseq-sr.yaml b/regression/presets/analyze/thermofisher-mouse-dna-igh-ampliseq-sr.yaml index a5d7d3d93..cbce93f1f 100644 --- a/regression/presets/analyze/thermofisher-mouse-dna-igh-ampliseq-sr.yaml +++ b/regression/presets/analyze/thermofisher-mouse-dna-igh-ampliseq-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-mouse-dna-tcb-ampliseq-sr.yaml b/regression/presets/analyze/thermofisher-mouse-dna-tcb-ampliseq-sr.yaml index a5d7d3d93..cbce93f1f 100644 --- a/regression/presets/analyze/thermofisher-mouse-dna-tcb-ampliseq-sr.yaml +++ b/regression/presets/analyze/thermofisher-mouse-dna-tcb-ampliseq-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-mouse-rna-igh-ampliseq-sr.yaml b/regression/presets/analyze/thermofisher-mouse-rna-igh-ampliseq-sr.yaml index a5d7d3d93..cbce93f1f 100644 --- a/regression/presets/analyze/thermofisher-mouse-rna-igh-ampliseq-sr.yaml +++ b/regression/presets/analyze/thermofisher-mouse-rna-igh-ampliseq-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/thermofisher-mouse-rna-tcb-ampliseq-sr.yaml b/regression/presets/analyze/thermofisher-mouse-rna-tcb-ampliseq-sr.yaml index a5d7d3d93..cbce93f1f 100644 --- a/regression/presets/analyze/thermofisher-mouse-rna-tcb-ampliseq-sr.yaml +++ b/regression/presets/analyze/thermofisher-mouse-rna-tcb-ampliseq-sr.yaml @@ -27,6 +27,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -70,6 +71,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -104,7 +106,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -184,18 +185,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/umi-guided-consensus-test.yaml b/regression/presets/analyze/umi-guided-consensus-test.yaml index f4b2a68a2..eed34bc71 100644 --- a/regression/presets/analyze/umi-guided-consensus-test.yaml +++ b/regression/presets/analyze/umi-guided-consensus-test.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: type: kaligner @@ -68,6 +69,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 60 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -95,6 +97,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -123,7 +126,6 @@ align: includeDScore: true includeCScore: true minSumScore: 200.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: true allowNoCDR3PartAlignments: false @@ -245,18 +247,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml b/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml index 867e6b8bb..6dfb4293a 100644 --- a/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml +++ b/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/presets/analyze/vergani-et-al-2017-full-length.yaml b/regression/presets/analyze/vergani-et-al-2017-full-length.yaml index 523fda3ba..4aef60284 100644 --- a/regression/presets/analyze/vergani-et-al-2017-full-length.yaml +++ b/regression/presets/analyze/vergani-et-al-2017-full-length.yaml @@ -30,6 +30,7 @@ align: geneFeatureToAlign: VTranscriptWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -73,6 +74,7 @@ align: geneFeatureToAlign: JRegionWithP minSumScore: 150 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner2 mapperNValue: 8 @@ -106,6 +108,7 @@ align: geneFeatureToAlign: CExon1 minSumScore: 40 relativeMinScore: 0.97 + maxHits: 5 parameters: type: kaligner mapperKValue: 5 @@ -134,7 +137,6 @@ align: includeDScore: false includeCScore: false minSumScore: 120.0 - maxHits: 5 relativeMinVFR3CDR3Score: 0.7 allowPartialAlignments: false allowNoCDR3PartAlignments: false @@ -273,18 +275,12 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 cParameters: - relativeMinScore: null - scoring: null maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 dParameters: diff --git a/regression/schemas/analyzeBundle/parameters/align.schema.yaml b/regression/schemas/analyzeBundle/parameters/align.schema.yaml index 04b11a5f4..e62fe180b 100644 --- a/regression/schemas/analyzeBundle/parameters/align.schema.yaml +++ b/regression/schemas/analyzeBundle/parameters/align.schema.yaml @@ -217,8 +217,6 @@ properties: enum: - Unknown - R1V - maxHits: - type: integer mergerParameters: type: object properties: diff --git a/regression/schemas/parametersForOverride/VDJCAlignerParameters.schema.yaml b/regression/schemas/parametersForOverride/VDJCAlignerParameters.schema.yaml index f031f0858..4d5bd54c5 100644 --- a/regression/schemas/parametersForOverride/VDJCAlignerParameters.schema.yaml +++ b/regression/schemas/parametersForOverride/VDJCAlignerParameters.schema.yaml @@ -30,8 +30,6 @@ properties: enum: - Unknown - R1V - maxHits: - type: integer mergerParameters: type: object properties: From ea8d28fbda78f26555225af43d28ef4760f58097 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 22 Feb 2024 17:36:24 +0100 Subject: [PATCH 6/7] fix test --- .../mixcr/vdjaligners/VDJCAlignerParametersTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java index f68147777..cc2b3e89a 100644 --- a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java +++ b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java @@ -44,7 +44,7 @@ public void test1() throws Exception { LinearGapAlignmentScoring.getNucleotideBLASTScoring()), null, null), VJAlignmentOrder.JThenV, VDJCLibraryStructure.Unknown, false, false, - 120.0f, 5, 0.7f, false, false, false, PairedEndReadsLayout.Opposite, new MergerParameters( + 120.0f, 0, 0.7f, false, false, false, PairedEndReadsLayout.Opposite, new MergerParameters( QualityMergingAlgorithm.SumSubtraction, null, 12, 12, null, 0.12, Unweighted), false, 5, 120, 10, true, true, true); String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs); From c3cf2fc59115d3676e7c9dd13baa367244126ab3 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Fri, 23 Feb 2024 11:43:24 +0100 Subject: [PATCH 7/7] fix assemble contigs --- .../com/milaboratory/mixcr/cli/CommandAssembleContigs.kt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssembleContigs.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssembleContigs.kt index fbfc7bf43..3f9e5349b 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssembleContigs.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandAssembleContigs.kt @@ -194,13 +194,13 @@ object CommandAssembleContigs { .use { debugReport -> footer = reader.footer ordering = reader.ordering + header = reader.header val cloneFactory = CloneFactory( - reader.assemblerParameters.cloneFactoryParameters, + reader.assemblerParameters.updateFrom(header.alignerParameters).cloneFactoryParameters, reader.assemblingFeatures, reader.usedGenes, reader.header.featuresToAlignMap ) - header = reader.header genes = reader.usedGenes IOUtil.registerGeneReferences(tmpOut, genes, header)