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move maxHits params into separate genes #1545

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merged 9 commits into from
Feb 26, 2024
Merged

move maxHits params into separate genes #1545

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bb6f2d2
move maxHits params into separate genes
gnefedev Feb 21, 2024
e9774cb
update version
gnefedev Feb 22, 2024
1990691
update version
gnefedev Feb 22, 2024
ca6b59b
update version
gnefedev Feb 22, 2024
54327e8
regression tests automated change
gnefedev Feb 22, 2024
621a2bd
Merge pull request #1546 from milaboratory/mixcr-regression-tests/max…
gnefedev Feb 22, 2024
ea8d28f
fix test
gnefedev Feb 22, 2024
3794dca
Merge remote-tracking branch 'origin/max-hits-params' into max-hits-p…
gnefedev Feb 22, 2024
c3cf2fc
fix assemble contigs
gnefedev Feb 23, 2024
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2 changes: 1 addition & 1 deletion build.gradle.kts
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Original file line number Diff line number Diff line change
Expand Up @@ -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 = "4.6.0-70-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)
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10 changes: 3 additions & 7 deletions regression/presets/analyze/10x-5gex-cdr3.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ align:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
type: kaligner2
Expand Down Expand Up @@ -82,6 +83,7 @@ align:
geneFeatureToAlign: JRegionWithP
minSumScore: 150
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner2
mapperNValue: 8
Expand Down Expand Up @@ -115,6 +117,7 @@ align:
geneFeatureToAlign: CExon1
minSumScore: 40
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner
mapperKValue: 5
Expand Down Expand Up @@ -143,7 +146,6 @@ align:
includeDScore: false
includeCScore: false
minSumScore: 120.0
maxHits: 5
relativeMinVFR3CDR3Score: 0.7
allowPartialAlignments: true
allowNoCDR3PartAlignments: true
Expand Down Expand Up @@ -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:
Expand Down
10 changes: 3 additions & 7 deletions regression/presets/analyze/10x-5gex-full-length.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ align:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
type: kaligner2
Expand Down Expand Up @@ -82,6 +83,7 @@ align:
geneFeatureToAlign: JRegionWithP
minSumScore: 150
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner2
mapperNValue: 8
Expand Down Expand Up @@ -115,6 +117,7 @@ align:
geneFeatureToAlign: CExon1
minSumScore: 40
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner
mapperKValue: 5
Expand Down Expand Up @@ -143,7 +146,6 @@ align:
includeDScore: false
includeCScore: false
minSumScore: 120.0
maxHits: 5
relativeMinVFR3CDR3Score: 0.7
allowPartialAlignments: true
allowNoCDR3PartAlignments: true
Expand Down Expand Up @@ -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:
Expand Down
10 changes: 3 additions & 7 deletions regression/presets/analyze/10x-sc-5gex.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ align:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
type: kaligner2
Expand Down Expand Up @@ -82,6 +83,7 @@ align:
geneFeatureToAlign: JRegionWithP
minSumScore: 150
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner2
mapperNValue: 8
Expand Down Expand Up @@ -115,6 +117,7 @@ align:
geneFeatureToAlign: CExon1
minSumScore: 40
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner
mapperKValue: 5
Expand Down Expand Up @@ -143,7 +146,6 @@ align:
includeDScore: false
includeCScore: false
minSumScore: 120.0
maxHits: 5
relativeMinVFR3CDR3Score: 0.7
allowPartialAlignments: true
allowNoCDR3PartAlignments: true
Expand Down Expand Up @@ -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:
Expand Down
10 changes: 3 additions & 7 deletions regression/presets/analyze/10x-sc-xcr-vdj.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ align:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
type: kaligner2
Expand Down Expand Up @@ -82,6 +83,7 @@ align:
geneFeatureToAlign: JRegionWithP
minSumScore: 150
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner2
mapperNValue: 8
Expand Down Expand Up @@ -115,6 +117,7 @@ align:
geneFeatureToAlign: CExon1
minSumScore: 40
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner
mapperKValue: 5
Expand Down Expand Up @@ -143,7 +146,6 @@ align:
includeDScore: false
includeCScore: false
minSumScore: 120.0
maxHits: 5
relativeMinVFR3CDR3Score: 0.7
allowPartialAlignments: true
allowNoCDR3PartAlignments: true
Expand Down Expand Up @@ -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:
Expand Down
10 changes: 3 additions & 7 deletions regression/presets/analyze/10x-vdj-bcr-full-length.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ align:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
type: kaligner2
Expand Down Expand Up @@ -82,6 +83,7 @@ align:
geneFeatureToAlign: JRegionWithP
minSumScore: 150
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner2
mapperNValue: 8
Expand Down Expand Up @@ -115,6 +117,7 @@ align:
geneFeatureToAlign: CExon1
minSumScore: 40
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner
mapperKValue: 5
Expand Down Expand Up @@ -143,7 +146,6 @@ align:
includeDScore: false
includeCScore: false
minSumScore: 120.0
maxHits: 5
relativeMinVFR3CDR3Score: 0.7
allowPartialAlignments: true
allowNoCDR3PartAlignments: true
Expand Down Expand Up @@ -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:
Expand Down
10 changes: 3 additions & 7 deletions regression/presets/analyze/10x-vdj-bcr.yaml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ align:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
type: kaligner2
Expand Down Expand Up @@ -82,6 +83,7 @@ align:
geneFeatureToAlign: JRegionWithP
minSumScore: 150
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner2
mapperNValue: 8
Expand Down Expand Up @@ -115,6 +117,7 @@ align:
geneFeatureToAlign: CExon1
minSumScore: 40
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner
mapperKValue: 5
Expand Down Expand Up @@ -143,7 +146,6 @@ align:
includeDScore: false
includeCScore: false
minSumScore: 120.0
maxHits: 5
relativeMinVFR3CDR3Score: 0.7
allowPartialAlignments: true
allowNoCDR3PartAlignments: true
Expand Down Expand Up @@ -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:
Expand Down
10 changes: 3 additions & 7 deletions regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ align:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
type: kaligner2
Expand Down Expand Up @@ -82,6 +83,7 @@ align:
geneFeatureToAlign: JRegionWithP
minSumScore: 150
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner2
mapperNValue: 8
Expand Down Expand Up @@ -115,6 +117,7 @@ align:
geneFeatureToAlign: CExon1
minSumScore: 40
relativeMinScore: 0.97
maxHits: 5
parameters:
type: kaligner
mapperKValue: 5
Expand Down Expand Up @@ -143,7 +146,6 @@ align:
includeDScore: false
includeCScore: false
minSumScore: 120.0
maxHits: 5
relativeMinVFR3CDR3Score: 0.7
allowPartialAlignments: true
allowNoCDR3PartAlignments: true
Expand Down Expand Up @@ -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:
Expand Down
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