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Regression tests changes in the contigs-per-cell #1595

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Regression tests changes in the contigs-per-cell #1595

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25 changes: 22 additions & 3 deletions regression/presets/analyze/10x-5gex-cdr3.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
flags:
- species
- assembleContigsByOrByCell
pipeline:
- align
- refineTagsAndSort
Expand Down Expand Up @@ -37,7 +38,7 @@ align:
vParameters:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
relativeMinScore: 0.9
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
Expand All @@ -56,7 +57,7 @@ align:
mapperMaxClusterIndels: 4
mapperKMersPerPosition: 4
mapperAbsoluteMinScore: 250
mapperRelativeMinScore: 0.75
mapperRelativeMinScore: 0.9
mapperMinSeedsDistance: 6
mapperMaxSeedsDistance: 6
alignmentStopPenalty: 0
Expand All @@ -69,6 +70,7 @@ align:
subsMatrix: "simple(match = 10, mismatch = -19)"
gapOpenPenalty: -62
gapExtensionPenalty: -11
rightForceRealignmentTrigger: CDR3Begin(-6)
dParameters:
geneFeatureToAlign: DRegionWithP
relativeMinScore: 0.85
Expand Down Expand Up @@ -250,6 +252,7 @@ assemble:
backgroundIndelRate: 2.0E-4
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.7
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
Expand All @@ -270,7 +273,7 @@ assemble:
preClusteringScoreFilteringRatio: 2.0
preClusteringCountFilteringRatio: 2.0
addReadsCountOnClustering: false
badQualityThreshold: 15
badQualityThreshold: 10
maxBadPointsPercent: 0.7
mappingThreshold: 2of5
minimalQuality: 20
Expand Down Expand Up @@ -298,6 +301,22 @@ assembleContigs:
minimalContigLength: 20
alignedRegionsOnly: false
discardAmbiguousNucleotideCalls: false
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.97
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
cParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
dParameters:
relativeMinScore: null
absoluteMinScore: null
maxHits: null
scoring: null
assembleCells:
algorithm:
type: SingleCellGroupingByOverlappingCellIds
Expand Down
24 changes: 21 additions & 3 deletions regression/presets/analyze/10x-5gex-full-length.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ align:
vParameters:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
relativeMinScore: 0.9
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
Expand All @@ -56,7 +56,7 @@ align:
mapperMaxClusterIndels: 4
mapperKMersPerPosition: 4
mapperAbsoluteMinScore: 250
mapperRelativeMinScore: 0.75
mapperRelativeMinScore: 0.9
mapperMinSeedsDistance: 6
mapperMaxSeedsDistance: 6
alignmentStopPenalty: 0
Expand All @@ -69,6 +69,7 @@ align:
subsMatrix: "simple(match = 10, mismatch = -19)"
gapOpenPenalty: -62
gapExtensionPenalty: -11
rightForceRealignmentTrigger: CDR3Begin(-6)
dParameters:
geneFeatureToAlign: DRegionWithP
relativeMinScore: 0.85
Expand Down Expand Up @@ -250,6 +251,7 @@ assemble:
backgroundIndelRate: 2.0E-4
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.7
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
Expand All @@ -270,7 +272,7 @@ assemble:
preClusteringScoreFilteringRatio: 2.0
preClusteringCountFilteringRatio: 2.0
addReadsCountOnClustering: false
badQualityThreshold: 15
badQualityThreshold: 10
maxBadPointsPercent: 0.7
mappingThreshold: 2of5
minimalQuality: 20
Expand Down Expand Up @@ -302,6 +304,22 @@ assembleContigs:
minimalContigLength: 20
alignedRegionsOnly: true
discardAmbiguousNucleotideCalls: false
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.97
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
cParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
dParameters:
relativeMinScore: null
absoluteMinScore: null
maxHits: null
scoring: null
assembleCells:
algorithm:
type: SingleCellGroupingByOverlappingCellIds
Expand Down
25 changes: 22 additions & 3 deletions regression/presets/analyze/10x-sc-5gex.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
flags:
- species
- assembleContigsByOrByCell
pipeline:
- align
- refineTagsAndSort
Expand Down Expand Up @@ -37,7 +38,7 @@ align:
vParameters:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
relativeMinScore: 0.9
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
Expand All @@ -56,7 +57,7 @@ align:
mapperMaxClusterIndels: 4
mapperKMersPerPosition: 4
mapperAbsoluteMinScore: 250
mapperRelativeMinScore: 0.75
mapperRelativeMinScore: 0.9
mapperMinSeedsDistance: 6
mapperMaxSeedsDistance: 6
alignmentStopPenalty: 0
Expand All @@ -69,6 +70,7 @@ align:
subsMatrix: "simple(match = 10, mismatch = -19)"
gapOpenPenalty: -62
gapExtensionPenalty: -11
rightForceRealignmentTrigger: CDR3Begin(-6)
dParameters:
geneFeatureToAlign: DRegionWithP
relativeMinScore: 0.85
Expand Down Expand Up @@ -250,6 +252,7 @@ assemble:
backgroundIndelRate: 2.0E-4
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.7
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
Expand All @@ -270,7 +273,7 @@ assemble:
preClusteringScoreFilteringRatio: 2.0
preClusteringCountFilteringRatio: 2.0
addReadsCountOnClustering: false
badQualityThreshold: 15
badQualityThreshold: 10
maxBadPointsPercent: 0.7
mappingThreshold: 2of5
minimalQuality: 20
Expand Down Expand Up @@ -298,6 +301,22 @@ assembleContigs:
minimalContigLength: 20
alignedRegionsOnly: false
discardAmbiguousNucleotideCalls: false
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.97
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
cParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
dParameters:
relativeMinScore: null
absoluteMinScore: null
maxHits: null
scoring: null
assembleCells:
algorithm:
type: SingleCellGroupingByOverlappingCellIds
Expand Down
25 changes: 22 additions & 3 deletions regression/presets/analyze/10x-sc-xcr-vdj.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
flags:
- species
- assembleContigsByOrByCell
pipeline:
- align
- refineTagsAndSort
Expand Down Expand Up @@ -37,7 +38,7 @@ align:
vParameters:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
relativeMinScore: 0.9
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
Expand All @@ -56,7 +57,7 @@ align:
mapperMaxClusterIndels: 4
mapperKMersPerPosition: 4
mapperAbsoluteMinScore: 250
mapperRelativeMinScore: 0.75
mapperRelativeMinScore: 0.9
mapperMinSeedsDistance: 6
mapperMaxSeedsDistance: 6
alignmentStopPenalty: 0
Expand All @@ -69,6 +70,7 @@ align:
subsMatrix: "simple(match = 10, mismatch = -19)"
gapOpenPenalty: -62
gapExtensionPenalty: -11
rightForceRealignmentTrigger: CDR3Begin(-6)
dParameters:
geneFeatureToAlign: DRegionWithP
relativeMinScore: 0.85
Expand Down Expand Up @@ -356,6 +358,7 @@ assemble:
backgroundIndelRate: 2.0E-4
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.7
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
Expand All @@ -376,7 +379,7 @@ assemble:
preClusteringScoreFilteringRatio: 2.0
preClusteringCountFilteringRatio: 2.0
addReadsCountOnClustering: false
badQualityThreshold: 15
badQualityThreshold: 10
maxBadPointsPercent: 0.7
mappingThreshold: 2of5
minimalQuality: 20
Expand Down Expand Up @@ -432,6 +435,22 @@ assembleContigs:
minimalContigLength: 20
alignedRegionsOnly: false
discardAmbiguousNucleotideCalls: false
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.97
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
cParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
dParameters:
relativeMinScore: null
absoluteMinScore: null
maxHits: null
scoring: null
assembleCells:
algorithm:
type: SingleCellGroupingByOverlappingCellIds
Expand Down
24 changes: 21 additions & 3 deletions regression/presets/analyze/10x-vdj-bcr-full-length.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ align:
vParameters:
geneFeatureToAlign: VTranscriptWithP
minSumScore: 60
relativeMinScore: 0.97
relativeMinScore: 0.9
maxHits: 5
edgeRealignmentMinScoreOverride: 35
parameters:
Expand All @@ -56,7 +56,7 @@ align:
mapperMaxClusterIndels: 4
mapperKMersPerPosition: 4
mapperAbsoluteMinScore: 250
mapperRelativeMinScore: 0.75
mapperRelativeMinScore: 0.9
mapperMinSeedsDistance: 6
mapperMaxSeedsDistance: 6
alignmentStopPenalty: 0
Expand All @@ -69,6 +69,7 @@ align:
subsMatrix: "simple(match = 10, mismatch = -19)"
gapOpenPenalty: -62
gapExtensionPenalty: -11
rightForceRealignmentTrigger: CDR3Begin(-6)
dParameters:
geneFeatureToAlign: DRegionWithP
relativeMinScore: 0.85
Expand Down Expand Up @@ -356,6 +357,7 @@ assemble:
backgroundIndelRate: 2.0E-4
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.7
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
Expand All @@ -376,7 +378,7 @@ assemble:
preClusteringScoreFilteringRatio: 2.0
preClusteringCountFilteringRatio: 2.0
addReadsCountOnClustering: false
badQualityThreshold: 15
badQualityThreshold: 10
maxBadPointsPercent: 0.7
mappingThreshold: 2of5
minimalQuality: 20
Expand Down Expand Up @@ -436,6 +438,22 @@ assembleContigs:
minimalContigLength: 20
alignedRegionsOnly: true
discardAmbiguousNucleotideCalls: false
cloneFactoryParameters:
vParameters:
relativeMinScore: 0.97
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
jParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
cParameters:
maxAlignmentWidthLinear: 5
maxAlignmentWidthAffine: 500
dParameters:
relativeMinScore: null
absoluteMinScore: null
maxHits: null
scoring: null
assembleCells:
algorithm:
type: SingleCellGroupingByOverlappingCellIds
Expand Down