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Merge pull request #1546 from milaboratory/mixcr-regression-tests/max…
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…-hits-params

Regression tests changes in the max-hits-params
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@gnefedev
gnefedev authored Feb 22, 2024
2 parents ca6b59b + 54327e8 commit 621a2bd
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Showing 213 changed files with 583 additions and 1,481 deletions.
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:
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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
View file
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
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
View file
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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