From 0965d37f4c131d6b1f526a060986bd2e1918f650 Mon Sep 17 00:00:00 2001 From: gnefedev <14794051+gnefedev@users.noreply.github.com> Date: Mon, 29 Apr 2024 15:58:02 +0000 Subject: [PATCH] regression tests automated change --- regression/presets/analyze/10x-5gex-cdr3.yaml | 25 +- .../presets/analyze/10x-5gex-full-length.yaml | 24 +- regression/presets/analyze/10x-sc-5gex.yaml | 25 +- .../presets/analyze/10x-sc-xcr-vdj.yaml | 25 +- .../analyze/10x-vdj-bcr-full-length.yaml | 24 +- regression/presets/analyze/10x-vdj-bcr.yaml | 25 +- .../10x-vdj-tcr-alias-multi-barcode-test.yaml | 25 +- .../analyze/10x-vdj-tcr-full-length.yaml | 24 +- .../10x-vdj-tcr-multi-barcode-test.yaml | 8 +- .../presets/analyze/10x-vdj-tcr-qc-test.yaml | 25 +- regression/presets/analyze/10x-vdj-tcr.yaml | 25 +- .../bd-rhapsody-human-bcr-full-length.yaml | 36 +- .../bd-rhapsody-human-tcr-full-length.yaml | 36 +- .../bd-rhapsody-mouse-bcr-full-length.yaml | 36 +- .../bd-rhapsody-mouse-tcr-full-length.yaml | 36 +- ...rhapsody-full-length-enhanced-bead-v2.yaml | 36 +- .../bd-sc-xcr-rhapsody-full-length.yaml | 36 +- regression/presets/analyze/exome-seq.yaml | 1 + .../analyze/generic-amplicon-with-umi.yaml | 4 +- .../presets/analyze/generic-amplicon.yaml | 4 +- .../analyze/generic-bcr-amplicon-umi.yaml | 4 +- .../presets/analyze/generic-bcr-amplicon.yaml | 4 +- ...eric-ht-single-cell-amplicon-with-umi.yaml | 4 +- .../generic-ht-single-cell-amplicon.yaml | 4 +- ...ic-ht-single-cell-fragmented-with-umi.yaml | 25 +- .../generic-ht-single-cell-fragmented.yaml | 25 +- ...eric-lt-single-cell-amplicon-with-umi.yaml | 4 +- .../generic-lt-single-cell-amplicon.yaml | 4 +- ...ic-lt-single-cell-fragmented-with-umi.yaml | 25 +- .../generic-lt-single-cell-fragmented.yaml | 25 +- .../presets/analyze/generic-ont-with-umi.yaml | 1 + regression/presets/analyze/generic-ont.yaml | 1 + .../analyze/generic-pacbio-with-umi.yaml | 4 +- .../presets/analyze/generic-pacbio.yaml | 4 +- .../generic-single-cell-gex-with-umi.yaml | 25 +- .../analyze/generic-single-cell-gex.yaml | 25 +- ...ric-tcr-amplicon-separate-samples-umi.yaml | 4 +- .../analyze/generic-tcr-amplicon-umi.yaml | 4 +- .../presets/analyze/generic-tcr-amplicon.yaml | 4 +- .../analyze/ont-rna-seq-vdj-full-length.yaml | 1 + regression/presets/analyze/ont-rna-seq.yaml | 1 + .../presets/analyze/parse-bio-vdj-3gex.yaml | 25 +- .../parsebio-sc-3gex-evercode-wt-mega.yaml | 25 +- .../parsebio-sc-3gex-evercode-wt-mini.yaml | 25 +- .../analyze/parsebio-sc-3gex-evercode-wt.yaml | 25 +- .../presets/analyze/pereshlop-test.yaml | 3 +- regression/presets/analyze/rna-seq.yaml | 1 + regression/presets/analyze/seq-well-vdj.yaml | 4 +- .../presets/analyze/seqwell-vdj-cdr3.yaml | 4 +- .../single-cell-as-sample-no-split.yaml | 8 +- .../analyze/single-cell-as-sample-split.yaml | 8 +- .../analyze/singleron-2.0.1-vdj-cdr3.yaml | 6 +- .../singleron-human-sc-xcr-gexscope-vdj.yaml | 6 +- .../presets/analyze/smart-seq2-vdj.yaml | 25 +- .../analyze/smartseq2-vdj-full-length.yaml | 25 +- .../presets/analyze/split-seq-3gex.yaml | 25 +- .../presets/analyze/split-seq-vdj-3gex.yaml | 25 +- .../test-mikelov-et-al-2021-with-contigs.yaml | 6 +- .../analyze/test-subCloningRegions.yaml | 3 +- .../presets/analyze/test-tag-from-header.yaml | 6 +- .../analyze/umi-guided-consensus-test.yaml | 3 +- regression/presets/list.txt | 28 ++ regression/reports/baseSingleCell.raw.yaml | 344 +++++++++--------- .../reports/baseSingleCell.vdjcontigs.yaml | 336 +++++++++-------- 64 files changed, 1119 insertions(+), 525 deletions(-) diff --git a/regression/presets/analyze/10x-5gex-cdr3.yaml b/regression/presets/analyze/10x-5gex-cdr3.yaml index 470543341..4e1290153 100644 --- a/regression/presets/analyze/10x-5gex-cdr3.yaml +++ b/regression/presets/analyze/10x-5gex-cdr3.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -250,6 +252,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -270,7 +273,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 diff --git a/regression/presets/analyze/10x-5gex-full-length.yaml b/regression/presets/analyze/10x-5gex-full-length.yaml index 075d474b9..3dc8b3ef6 100644 --- a/regression/presets/analyze/10x-5gex-full-length.yaml +++ b/regression/presets/analyze/10x-5gex-full-length.yaml @@ -37,7 +37,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +56,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +69,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -250,6 +251,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -270,7 +272,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 diff --git a/regression/presets/analyze/10x-sc-5gex.yaml b/regression/presets/analyze/10x-sc-5gex.yaml index 470543341..4e1290153 100644 --- a/regression/presets/analyze/10x-sc-5gex.yaml +++ b/regression/presets/analyze/10x-sc-5gex.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -250,6 +252,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -270,7 +273,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 diff --git a/regression/presets/analyze/10x-sc-xcr-vdj.yaml b/regression/presets/analyze/10x-sc-xcr-vdj.yaml index c34cf2126..e22fa308f 100644 --- a/regression/presets/analyze/10x-sc-xcr-vdj.yaml +++ b/regression/presets/analyze/10x-sc-xcr-vdj.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -356,6 +358,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -376,7 +379,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml index 53099685e..0cb91b0cb 100644 --- a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml @@ -37,7 +37,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +56,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +69,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -356,6 +357,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -376,7 +378,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml index c34cf2126..e22fa308f 100644 --- a/regression/presets/analyze/10x-vdj-bcr.yaml +++ b/regression/presets/analyze/10x-vdj-bcr.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -356,6 +358,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -376,7 +379,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 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 dbac46f6b..1436e71ae 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 @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -341,8 +343,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: @@ -464,6 +465,22 @@ 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 diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml index 53099685e..0cb91b0cb 100644 --- a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml @@ -37,7 +37,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +56,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +69,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -356,6 +357,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -376,7 +378,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 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 963a48dda..ed88d6e01 100644 --- a/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml @@ -31,7 +31,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -50,7 +50,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -63,6 +63,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -288,8 +289,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml index 25a5bc5fa..b1ff87c07 100644 --- a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -39,7 +40,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -58,7 +59,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -71,6 +72,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -358,6 +360,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -378,7 +381,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -434,6 +437,22 @@ 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 diff --git a/regression/presets/analyze/10x-vdj-tcr.yaml b/regression/presets/analyze/10x-vdj-tcr.yaml index c34cf2126..e22fa308f 100644 --- a/regression/presets/analyze/10x-vdj-tcr.yaml +++ b/regression/presets/analyze/10x-vdj-tcr.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -356,6 +358,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -376,7 +379,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 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 a84af4c43..064961a35 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml @@ -670,7 +670,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -689,7 +689,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -702,6 +702,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -956,6 +957,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -976,7 +978,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -1025,16 +1027,36 @@ assembleContigs: minimalMeanNormalizedQuality: 5.0 outputMinimalQualityShare: 0.75 outputMinimalSumQuality: 0 - subCloningRegions: null - assemblingRegions: null + subCloningRegions: + - VDJRegion + assemblingRegions: + - VDJRegion postFiltering: - type: NoFiltering + type: OnlyUnambiguouslyCovering + geneFeatures: + - VDJRegion trimmingParameters: averageQualityThreshold: 10.0 windowSize: 8 minimalContigLength: 20 - alignedRegionsOnly: false + 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 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 a84af4c43..064961a35 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml @@ -670,7 +670,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -689,7 +689,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -702,6 +702,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -956,6 +957,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -976,7 +978,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -1025,16 +1027,36 @@ assembleContigs: minimalMeanNormalizedQuality: 5.0 outputMinimalQualityShare: 0.75 outputMinimalSumQuality: 0 - subCloningRegions: null - assemblingRegions: null + subCloningRegions: + - VDJRegion + assemblingRegions: + - VDJRegion postFiltering: - type: NoFiltering + type: OnlyUnambiguouslyCovering + geneFeatures: + - VDJRegion trimmingParameters: averageQualityThreshold: 10.0 windowSize: 8 minimalContigLength: 20 - alignedRegionsOnly: false + 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 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 a84af4c43..064961a35 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml @@ -670,7 +670,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -689,7 +689,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -702,6 +702,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -956,6 +957,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -976,7 +978,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -1025,16 +1027,36 @@ assembleContigs: minimalMeanNormalizedQuality: 5.0 outputMinimalQualityShare: 0.75 outputMinimalSumQuality: 0 - subCloningRegions: null - assemblingRegions: null + subCloningRegions: + - VDJRegion + assemblingRegions: + - VDJRegion postFiltering: - type: NoFiltering + type: OnlyUnambiguouslyCovering + geneFeatures: + - VDJRegion trimmingParameters: averageQualityThreshold: 10.0 windowSize: 8 minimalContigLength: 20 - alignedRegionsOnly: false + 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 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 a84af4c43..064961a35 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml @@ -670,7 +670,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -689,7 +689,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -702,6 +702,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -956,6 +957,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -976,7 +978,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -1025,16 +1027,36 @@ assembleContigs: minimalMeanNormalizedQuality: 5.0 outputMinimalQualityShare: 0.75 outputMinimalSumQuality: 0 - subCloningRegions: null - assemblingRegions: null + subCloningRegions: + - VDJRegion + assemblingRegions: + - VDJRegion postFiltering: - type: NoFiltering + type: OnlyUnambiguouslyCovering + geneFeatures: + - VDJRegion trimmingParameters: averageQualityThreshold: 10.0 windowSize: 8 minimalContigLength: 20 - alignedRegionsOnly: false + 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 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 bfcc0e263..331997896 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 @@ -2398,7 +2398,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -2417,7 +2417,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -2430,6 +2430,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -2684,6 +2685,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -2704,7 +2706,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -2753,16 +2755,36 @@ assembleContigs: minimalMeanNormalizedQuality: 5.0 outputMinimalQualityShare: 0.75 outputMinimalSumQuality: 0 - subCloningRegions: null - assemblingRegions: null + subCloningRegions: + - VDJRegion + assemblingRegions: + - VDJRegion postFiltering: - type: NoFiltering + type: OnlyUnambiguouslyCovering + geneFeatures: + - VDJRegion trimmingParameters: averageQualityThreshold: 10.0 windowSize: 8 minimalContigLength: 20 - alignedRegionsOnly: false + 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 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 a84af4c43..064961a35 100644 --- a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml +++ b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml @@ -670,7 +670,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -689,7 +689,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -702,6 +702,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -956,6 +957,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -976,7 +978,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -1025,16 +1027,36 @@ assembleContigs: minimalMeanNormalizedQuality: 5.0 outputMinimalQualityShare: 0.75 outputMinimalSumQuality: 0 - subCloningRegions: null - assemblingRegions: null + subCloningRegions: + - VDJRegion + assemblingRegions: + - VDJRegion postFiltering: - type: NoFiltering + type: OnlyUnambiguouslyCovering + geneFeatures: + - VDJRegion trimmingParameters: averageQualityThreshold: 10.0 windowSize: 8 minimalContigLength: 20 - alignedRegionsOnly: false + 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 diff --git a/regression/presets/analyze/exome-seq.yaml b/regression/presets/analyze/exome-seq.yaml index c0a520802..03fd245de 100644 --- a/regression/presets/analyze/exome-seq.yaml +++ b/regression/presets/analyze/exome-seq.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrMaxLength pipeline: - align - assemblePartial diff --git a/regression/presets/analyze/generic-amplicon-with-umi.yaml b/regression/presets/analyze/generic-amplicon-with-umi.yaml index 456b20ffa..b9f027d2e 100644 --- a/regression/presets/analyze/generic-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-amplicon-with-umi.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - materialType @@ -265,8 +266,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/generic-amplicon.yaml b/regression/presets/analyze/generic-amplicon.yaml index aa84fe9b1..bc5c8f6b8 100644 --- a/regression/presets/analyze/generic-amplicon.yaml +++ b/regression/presets/analyze/generic-amplicon.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - materialType @@ -202,8 +203,7 @@ assemble: cellLevel: false consensusAssemblerParameters: null cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/generic-bcr-amplicon-umi.yaml b/regression/presets/analyze/generic-bcr-amplicon-umi.yaml index 456b20ffa..b9f027d2e 100644 --- a/regression/presets/analyze/generic-bcr-amplicon-umi.yaml +++ b/regression/presets/analyze/generic-bcr-amplicon-umi.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - materialType @@ -265,8 +266,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/generic-bcr-amplicon.yaml b/regression/presets/analyze/generic-bcr-amplicon.yaml index aa84fe9b1..bc5c8f6b8 100644 --- a/regression/presets/analyze/generic-bcr-amplicon.yaml +++ b/regression/presets/analyze/generic-bcr-amplicon.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - materialType @@ -202,8 +203,7 @@ assemble: cellLevel: false consensusAssemblerParameters: null cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: 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 044edc64f..b09cb0938 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 @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - tagPattern @@ -308,8 +309,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml b/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml index 042818d66..42f092954 100644 --- a/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - tagPattern @@ -261,8 +262,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: 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 ac1e7ee4a..175464a44 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 @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell - tagPattern pipeline: - align @@ -38,7 +39,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -57,7 +58,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -70,6 +71,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -325,6 +327,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -345,7 +348,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -404,6 +407,22 @@ 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 diff --git a/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml b/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml index 1cc545357..27fa0dc49 100644 --- a/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell - tagPattern pipeline: - align @@ -38,7 +39,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -57,7 +58,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -70,6 +71,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -278,6 +280,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -298,7 +301,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -352,6 +355,22 @@ 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 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 84083f439..b4bf2e42e 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 @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode pipeline: @@ -275,8 +276,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml b/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml index b4e6b2799..e7dff00b4 100644 --- a/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode pipeline: @@ -232,8 +233,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: 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 b3acc864d..b8b2092ad 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 @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -292,6 +294,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -312,7 +315,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -371,6 +374,22 @@ 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 diff --git a/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml b/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml index dc7cadbb3..892c9ddf7 100644 --- a/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -249,6 +251,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -269,7 +272,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -323,6 +326,22 @@ 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 diff --git a/regression/presets/analyze/generic-ont-with-umi.yaml b/regression/presets/analyze/generic-ont-with-umi.yaml index 881e960c8..1325d0746 100644 --- a/regression/presets/analyze/generic-ont-with-umi.yaml +++ b/regression/presets/analyze/generic-ont-with-umi.yaml @@ -1,6 +1,7 @@ flags: - species - tagPattern + - assembleContigsByOrMaxLength pipeline: - align - refineTagsAndSort diff --git a/regression/presets/analyze/generic-ont.yaml b/regression/presets/analyze/generic-ont.yaml index 5d786aaf5..09f3d3a6c 100644 --- a/regression/presets/analyze/generic-ont.yaml +++ b/regression/presets/analyze/generic-ont.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrMaxLength pipeline: - align - assemble diff --git a/regression/presets/analyze/generic-pacbio-with-umi.yaml b/regression/presets/analyze/generic-pacbio-with-umi.yaml index 66ac58814..9ea705457 100644 --- a/regression/presets/analyze/generic-pacbio-with-umi.yaml +++ b/regression/presets/analyze/generic-pacbio-with-umi.yaml @@ -1,4 +1,5 @@ flags: + - assembleClonesBy - species - tagPattern pipeline: @@ -264,8 +265,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/generic-pacbio.yaml b/regression/presets/analyze/generic-pacbio.yaml index 809c4bc92..65d7ddce4 100644 --- a/regression/presets/analyze/generic-pacbio.yaml +++ b/regression/presets/analyze/generic-pacbio.yaml @@ -1,4 +1,5 @@ flags: + - assembleClonesBy - species pipeline: - align @@ -201,8 +202,7 @@ assemble: cellLevel: false consensusAssemblerParameters: null cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: 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 0dc1b1e2a..ae8f2af6d 100644 --- a/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml +++ b/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml @@ -1,6 +1,7 @@ flags: - species - tagPattern + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -38,7 +39,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -57,7 +58,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -70,6 +71,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -250,6 +252,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -270,7 +273,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -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 diff --git a/regression/presets/analyze/generic-single-cell-gex.yaml b/regression/presets/analyze/generic-single-cell-gex.yaml index 699d6566d..2cb487179 100644 --- a/regression/presets/analyze/generic-single-cell-gex.yaml +++ b/regression/presets/analyze/generic-single-cell-gex.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -249,6 +251,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -269,7 +272,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -297,6 +300,22 @@ 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 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 456b20ffa..b9f027d2e 100644 --- a/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - materialType @@ -265,8 +266,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/generic-tcr-amplicon-umi.yaml b/regression/presets/analyze/generic-tcr-amplicon-umi.yaml index 456b20ffa..b9f027d2e 100644 --- a/regression/presets/analyze/generic-tcr-amplicon-umi.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon-umi.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - materialType @@ -265,8 +266,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/generic-tcr-amplicon.yaml b/regression/presets/analyze/generic-tcr-amplicon.yaml index aa84fe9b1..bc5c8f6b8 100644 --- a/regression/presets/analyze/generic-tcr-amplicon.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon.yaml @@ -1,5 +1,6 @@ flags: - leftAlignmentMode + - assembleClonesBy - species - rightAlignmentMode - materialType @@ -202,8 +203,7 @@ assemble: cellLevel: false consensusAssemblerParameters: null cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: 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 5d786aaf5..09f3d3a6c 100644 --- a/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml +++ b/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrMaxLength pipeline: - align - assemble diff --git a/regression/presets/analyze/ont-rna-seq.yaml b/regression/presets/analyze/ont-rna-seq.yaml index 5d786aaf5..09f3d3a6c 100644 --- a/regression/presets/analyze/ont-rna-seq.yaml +++ b/regression/presets/analyze/ont-rna-seq.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrMaxLength pipeline: - align - assemble diff --git a/regression/presets/analyze/parse-bio-vdj-3gex.yaml b/regression/presets/analyze/parse-bio-vdj-3gex.yaml index a1bd96a95..56e905d59 100644 --- a/regression/presets/analyze/parse-bio-vdj-3gex.yaml +++ b/regression/presets/analyze/parse-bio-vdj-3gex.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -846,7 +847,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -865,7 +866,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -878,6 +879,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -1058,6 +1060,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -1078,7 +1081,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -1106,6 +1109,22 @@ 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 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 a1bd96a95..56e905d59 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -846,7 +847,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -865,7 +866,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -878,6 +879,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -1058,6 +1060,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -1078,7 +1081,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -1106,6 +1109,22 @@ 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 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 1311bee5a..446daa516 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -510,7 +511,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -529,7 +530,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -542,6 +543,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -722,6 +724,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -742,7 +745,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -770,6 +773,22 @@ 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 diff --git a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml index 58ea9e08a..ff3dc88a8 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -654,7 +655,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -673,7 +674,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -686,6 +687,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -866,6 +868,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -886,7 +889,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -914,6 +917,22 @@ 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 diff --git a/regression/presets/analyze/pereshlop-test.yaml b/regression/presets/analyze/pereshlop-test.yaml index 3d3978b28..6f04b994a 100644 --- a/regression/presets/analyze/pereshlop-test.yaml +++ b/regression/presets/analyze/pereshlop-test.yaml @@ -192,8 +192,7 @@ assemble: cellLevel: false consensusAssemblerParameters: null cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/rna-seq.yaml b/regression/presets/analyze/rna-seq.yaml index e3cfb4b8e..8111b9770 100644 --- a/regression/presets/analyze/rna-seq.yaml +++ b/regression/presets/analyze/rna-seq.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrMaxLength pipeline: - align - assemblePartial diff --git a/regression/presets/analyze/seq-well-vdj.yaml b/regression/presets/analyze/seq-well-vdj.yaml index ab21f751f..b9c52133f 100644 --- a/regression/presets/analyze/seq-well-vdj.yaml +++ b/regression/presets/analyze/seq-well-vdj.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleClonesBy pipeline: - align - refineTagsAndSort @@ -305,8 +306,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/seqwell-vdj-cdr3.yaml b/regression/presets/analyze/seqwell-vdj-cdr3.yaml index ab21f751f..b9c52133f 100644 --- a/regression/presets/analyze/seqwell-vdj-cdr3.yaml +++ b/regression/presets/analyze/seqwell-vdj-cdr3.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleClonesBy pipeline: - align - refineTagsAndSort @@ -305,8 +306,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: 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 57c7fe755..131fa1655 100644 --- a/regression/presets/analyze/single-cell-as-sample-no-split.yaml +++ b/regression/presets/analyze/single-cell-as-sample-no-split.yaml @@ -47,7 +47,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -66,7 +66,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -79,6 +79,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -274,8 +275,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/single-cell-as-sample-split.yaml b/regression/presets/analyze/single-cell-as-sample-split.yaml index a3d3989fd..06bdc1374 100644 --- a/regression/presets/analyze/single-cell-as-sample-split.yaml +++ b/regression/presets/analyze/single-cell-as-sample-split.yaml @@ -47,7 +47,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -66,7 +66,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -79,6 +79,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -266,8 +267,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: 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 7038cf98e..08be14c00 100644 --- a/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml +++ b/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml @@ -1,4 +1,5 @@ -flags: [] +flags: + - assembleClonesBy pipeline: - align - refineTagsAndSort @@ -276,8 +277,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: 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 7038cf98e..08be14c00 100644 --- a/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml +++ b/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml @@ -1,4 +1,5 @@ -flags: [] +flags: + - assembleClonesBy pipeline: - align - refineTagsAndSort @@ -276,8 +277,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: true cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/smart-seq2-vdj.yaml b/regression/presets/analyze/smart-seq2-vdj.yaml index 664146230..fbf07172a 100644 --- a/regression/presets/analyze/smart-seq2-vdj.yaml +++ b/regression/presets/analyze/smart-seq2-vdj.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -249,6 +251,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -269,7 +272,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -297,6 +300,22 @@ 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 diff --git a/regression/presets/analyze/smartseq2-vdj-full-length.yaml b/regression/presets/analyze/smartseq2-vdj-full-length.yaml index 664146230..fbf07172a 100644 --- a/regression/presets/analyze/smartseq2-vdj-full-length.yaml +++ b/regression/presets/analyze/smartseq2-vdj-full-length.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -37,7 +38,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -56,7 +57,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -69,6 +70,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -249,6 +251,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -269,7 +272,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -297,6 +300,22 @@ 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 diff --git a/regression/presets/analyze/split-seq-3gex.yaml b/regression/presets/analyze/split-seq-3gex.yaml index 3e275b680..a2ebf8aef 100644 --- a/regression/presets/analyze/split-seq-3gex.yaml +++ b/regression/presets/analyze/split-seq-3gex.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -652,7 +653,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -671,7 +672,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -684,6 +685,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -864,6 +866,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -884,7 +887,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -912,6 +915,22 @@ 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 diff --git a/regression/presets/analyze/split-seq-vdj-3gex.yaml b/regression/presets/analyze/split-seq-vdj-3gex.yaml index 3e275b680..a2ebf8aef 100644 --- a/regression/presets/analyze/split-seq-vdj-3gex.yaml +++ b/regression/presets/analyze/split-seq-vdj-3gex.yaml @@ -1,5 +1,6 @@ flags: - species + - assembleContigsByOrByCell pipeline: - align - refineTagsAndSort @@ -652,7 +653,7 @@ align: vParameters: geneFeatureToAlign: VTranscriptWithP minSumScore: 60 - relativeMinScore: 0.97 + relativeMinScore: 0.9 maxHits: 5 edgeRealignmentMinScoreOverride: 35 parameters: @@ -671,7 +672,7 @@ align: mapperMaxClusterIndels: 4 mapperKMersPerPosition: 4 mapperAbsoluteMinScore: 250 - mapperRelativeMinScore: 0.75 + mapperRelativeMinScore: 0.9 mapperMinSeedsDistance: 6 mapperMaxSeedsDistance: 6 alignmentStopPenalty: 0 @@ -684,6 +685,7 @@ align: subsMatrix: "simple(match = 10, mismatch = -19)" gapOpenPenalty: -62 gapExtensionPenalty: -11 + rightForceRealignmentTrigger: CDR3Begin(-6) dParameters: geneFeatureToAlign: DRegionWithP relativeMinScore: 0.85 @@ -864,6 +866,7 @@ assemble: backgroundIndelRate: 2.0E-4 cloneFactoryParameters: vParameters: + relativeMinScore: 0.7 maxAlignmentWidthLinear: 5 maxAlignmentWidthAffine: 500 jParameters: @@ -884,7 +887,7 @@ assemble: preClusteringScoreFilteringRatio: 2.0 preClusteringCountFilteringRatio: 2.0 addReadsCountOnClustering: false - badQualityThreshold: 15 + badQualityThreshold: 10 maxBadPointsPercent: 0.7 mappingThreshold: 2of5 minimalQuality: 20 @@ -912,6 +915,22 @@ 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 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 5b537edf3..2a445f96b 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 @@ -1,4 +1,5 @@ -flags: [] +flags: + - assembleClonesBy pipeline: - align - refineTagsAndSort @@ -287,8 +288,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/test-subCloningRegions.yaml b/regression/presets/analyze/test-subCloningRegions.yaml index 766b6f7d9..1d6d37d6f 100644 --- a/regression/presets/analyze/test-subCloningRegions.yaml +++ b/regression/presets/analyze/test-subCloningRegions.yaml @@ -201,8 +201,7 @@ assemble: cellLevel: false consensusAssemblerParameters: null cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/test-tag-from-header.yaml b/regression/presets/analyze/test-tag-from-header.yaml index 55dc4f780..6dcd8c423 100644 --- a/regression/presets/analyze/test-tag-from-header.yaml +++ b/regression/presets/analyze/test-tag-from-header.yaml @@ -1,4 +1,5 @@ -flags: [] +flags: + - assembleClonesBy pipeline: - align - assemble @@ -202,8 +203,7 @@ assemble: cellLevel: false consensusAssemblerParameters: null cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/analyze/umi-guided-consensus-test.yaml b/regression/presets/analyze/umi-guided-consensus-test.yaml index eed34bc71..73a1b9a0e 100644 --- a/regression/presets/analyze/umi-guided-consensus-test.yaml +++ b/regression/presets/analyze/umi-guided-consensus-test.yaml @@ -232,8 +232,7 @@ assemble: minTagSuffixShare: 0.0 isolateChains: false cloneAssemblerParameters: - assemblingFeatures: - - CDR3 + assemblingFeatures: null minimalClonalSequenceLength: 12 qualityAggregationType: BetaScore cloneClusteringParameters: diff --git a/regression/presets/list.txt b/regression/presets/list.txt index e2d2ae7f6..cde37c30a 100644 --- a/regression/presets/list.txt +++ b/regression/presets/list.txt @@ -2,23 +2,28 @@ Generic presets: generic-single-cell-gex (Generic single-cell gene expression) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) generic-ont (Oxford Nanopore data) Required args: --species + (--assemble-contigs-by |--assemble-longest-contigs) generic-pacbio-with-umi (PacBio data with UMIs) Required args: + --assemble-clonotypes-by --species --tag-pattern generic-lt-single-cell-fragmented (Generic low throughput shotgun single-cell) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) generic-amplicon (Generic amplicon) Required args: (--floating-left-alignment-boundary []|--rigid-left-alignment-boundary []) + --assemble-clonotypes-by --species (--floating-right-alignment-boundary (|)|--rigid-right-alignment-boundary [(|)]) (--dna|--rna) @@ -27,30 +32,36 @@ generic-ont-with-umi (Oxford Nanopore data with UMIs) Required args: --species --tag-pattern + (--assemble-contigs-by |--assemble-longest-contigs) generic-single-cell-gex-with-umi (Generic single-cell gene expression with UMIs) Required args: --species --tag-pattern + (--assemble-contigs-by |--assemble-contigs-by-cells) generic-ht-single-cell-fragmented-with-umi (Generic high throughput shotgun single-cell with UMIs) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) --tag-pattern smart-seq2-vdj (Smart-Seq2) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) generic-lt-single-cell-amplicon-with-umi (Generic low throughput amplicon single-cell with UMIs) Required args: (--floating-left-alignment-boundary []|--rigid-left-alignment-boundary []) + --assemble-clonotypes-by --species (--floating-right-alignment-boundary (|)|--rigid-right-alignment-boundary [(|)]) generic-amplicon-with-umi (Generic amplicon with UMI barcodes) Required args: (--floating-left-alignment-boundary []|--rigid-left-alignment-boundary []) + --assemble-clonotypes-by --species (--floating-right-alignment-boundary (|)|--rigid-right-alignment-boundary [(|)]) (--dna|--rna) @@ -59,36 +70,43 @@ generic-amplicon-with-umi (Generic amplicon with UMI barcodes) generic-ht-single-cell-fragmented (Generic high throughput shotgun single-cell) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) --tag-pattern generic-lt-single-cell-amplicon (Generic low throughput amplicon single-cell) Required args: (--floating-left-alignment-boundary []|--rigid-left-alignment-boundary []) + --assemble-clonotypes-by --species (--floating-right-alignment-boundary (|)|--rigid-right-alignment-boundary [(|)]) generic-ht-single-cell-amplicon-with-umi (Generic high throughput amplicon single-cell with UMIs) Required args: (--floating-left-alignment-boundary []|--rigid-left-alignment-boundary []) + --assemble-clonotypes-by --species (--floating-right-alignment-boundary (|)|--rigid-right-alignment-boundary [(|)]) --tag-pattern generic-pacbio (PacBio data) Required args: + --assemble-clonotypes-by --species rna-seq (RNA-Seq data) Required args: --species + (--assemble-contigs-by |--assemble-longest-contigs) exome-seq (Exome-Seq data) Required args: --species + (--assemble-contigs-by |--assemble-longest-contigs) generic-ht-single-cell-amplicon (Generic high throughput amplicon single-cell) Required args: (--floating-left-alignment-boundary []|--rigid-left-alignment-boundary []) + --assemble-clonotypes-by --species (--floating-right-alignment-boundary (|)|--rigid-right-alignment-boundary [(|)]) --tag-pattern @@ -96,6 +114,7 @@ generic-ht-single-cell-amplicon (Generic high throughput amplicon single-cell) generic-lt-single-cell-fragmented-with-umi (Generic low throughput shotgun single-cell with UMIs) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) -----Invivoscribe----- invivoscribe-human-dna-igk-lymphotrack (LymphoTrack IGK Assay Panel) @@ -224,12 +243,14 @@ vergani-et-al-2017-full-length (Vergani et al., 2017) seq-well-vdj (Seq-well VDJ) Required args: --species + --assemble-clonotypes-by mikelov-et-al-2021 (Mikelov et al., 2021) split-seq-3gex (SPLIT-seq 3' Gene expression) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) biomed2-human-rna-igkl (BIOMED2 IGK/IGL) @@ -249,14 +270,17 @@ biomed2-human-rna-trbdg (BIOMED2 TCR Beta/Delta/Gamma) parsebio-sc-3gex-evercode-wt (Evercode single-cell WT) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) parsebio-sc-3gex-evercode-wt-mini (Evercode single-cell WT Mini) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) parsebio-sc-3gex-evercode-wt-mega (Evercode single-cell WT Mega) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) -----BD biosciences----- bd-mouse-sc-xcr-rhapsody-cdr3 (Rhapsody Mouse VDJ CDR3 Assay) @@ -285,14 +309,18 @@ neb-mouse-rna-xcr-umi-nebnext (NEBNext® Immune Sequencing Kit (Mouse) BCR & TCR 10x-sc-5gex (5' Single cell gene expression) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) 10x-sc-xcr-vdj (5' Single cell VDJ) Required args: --species + (--assemble-contigs-by |--assemble-contigs-by-cells) -----AbHelix----- abhelix-human-rna-xcr (Human immunoglobulin repertoire) -----Singleron Biotechnologies----- singleron-human-sc-xcr-gexscope-vdj (GEXSCOPE Human Single Cell V(D)J Kit ) + Required args: + --assemble-clonotypes-by diff --git a/regression/reports/baseSingleCell.raw.yaml b/regression/reports/baseSingleCell.raw.yaml index 0536e6424..b33d94e6e 100644 --- a/regression/reports/baseSingleCell.raw.yaml +++ b/regression/reports/baseSingleCell.raw.yaml @@ -10,24 +10,24 @@ align: outputFiles: - baseSingleCell.raw.vdjca totalReadsProcessed: 46879 - aligned: 40525 - notAligned: 6354 + aligned: 40733 + notAligned: 6146 notAlignedReasons: - NoHits: 5776 + NoHits: 6094 FailedAfterAOverlap: 0 NoCDR3Parts: 0 NoVHits: 0 NoJHits: 0 VAndJOnDifferentTargets: 0 - LowTotalScore: 578 + LowTotalScore: 52 NoBarcode: 0 SampleNotMatched: 0 overlapped: 0 overlappedAligned: 0 overlappedNotAligned: 0 alignmentAidedOverlaps: 0 - noCDR3PartsAlignments: 17724 - partialAlignments: 22009 + noCDR3PartsAlignments: 17643 + partialAlignments: 22298 chimeras: 0 vChimeras: 0 jChimeras: 0 @@ -38,40 +38,30 @@ align: chainUsage: type: chainUsage chimeras: 0 - total: 40525 + total: 40733 chains: - IGH: - total: 21 - nonFunctional: 0 - isOOF: 0 - hasStops: 0 - IGK: - total: 17 - nonFunctional: 0 - isOOF: 0 - hasStops: 0 IGL: - total: 15 + total: 2 nonFunctional: 0 isOOF: 0 hasStops: 0 TRA: - total: 2589 + total: 2845 nonFunctional: 27 isOOF: 27 hasStops: 0 TRAD: - total: 2980 + total: 2970 nonFunctional: 0 isOOF: 0 hasStops: 0 TRB: - total: 34901 + total: 34915 nonFunctional: 3 isOOF: 1 hasStops: 2 TRG: - total: 2 + total: 1 nonFunctional: 0 isOOF: 0 hasStops: 0 @@ -149,8 +139,8 @@ assemble: type: preCloneAssemblerReport inputGroups: 3 groupsWithNoAssemblingFeature: 0 - inputAlignments: 28024 - inputAlignmentsWithAssemblingFeature: 936 + inputAlignments: 27498 + inputAlignmentsWithAssemblingFeature: 904 coreAlignmentsDroppedByUncertainChain: 0 corePreClonesDroppedByTagSuffix: 0 coreAlignmentsDroppedByTagSuffix: 0 @@ -159,38 +149,38 @@ assemble: "2": 1 "3": 2 assemblingFeatureSequencesInZeroPreClones: 0 - coreAlignments: 857 + coreAlignments: 825 tagConflicts: 1 geneAndTagConflicts: 1 geneConflicts: Variable: 1 discardedCoreAlignments: 79 - empiricallyAssignedAlignments: 13109 - vjEmpiricallyAssignedAlignments: 8 + empiricallyAssignedAlignments: 12371 + vjEmpiricallyAssignedAlignments: 10 tagEmpiricallyAssignedAlignments: 0 - geneAndTagEmpiricallyAssignedAlignments: 13101 + geneAndTagEmpiricallyAssignedAlignments: 12361 empiricalAssignmentConflicts: 0 ignoredAlignments: 0 - unassignedAlignments: 14058 - totalReadsProcessed: 46737 + unassignedAlignments: 14302 + totalReadsProcessed: 46740 totalAlignmentsProcessed: 8 - totalAlignedReadsProcessed: 14108 - initialClonesCreated: 7 - readsDroppedNoTargetSequence: 27088 + totalAlignedReadsProcessed: 13335 + initialClonesCreated: 8 + readsDroppedNoTargetSequence: 26594 readsDroppedTooShortClonalSequence: 0 readsDroppedLowQuality: 0 - coreReads: 14107 - readsDroppedFailedMapping: 1 + coreReads: 13334 + readsDroppedFailedMapping: 0 lowQualityRescued: 0 clonesClustered: 0 readsClustered: 0 clones: 7 - clonesDroppedAsLowQuality: 0 + clonesDroppedAsLowQuality: 1 clonesPreClustered: 0 readsPreClustered: 0 - readsInClones: 14107 - readsInClonesBeforeClustering: 14107 - readsDroppedWithLowQualityClones: 0 + readsInClones: 13334 + readsInClonesBeforeClustering: 13334 + readsDroppedWithLowQualityClones: 1 clonalChainUsage: type: chainUsage chimeras: 0 @@ -219,8 +209,8 @@ assemble: - allTags:Cell numberOfGroups: 7 numberOfGroupsAccepted: 7 - totalWeight: 14107.0 - totalWeightAccepted: 14107.0 + totalWeight: 13334.0 + totalWeightAccepted: 13334.0 operatorReports: - operatorReport: type: generic_hist_report @@ -238,21 +228,21 @@ assembleContigs: - baseSingleCell.raw.clna outputFiles: - baseSingleCell.raw.contigs.clns - clonesWithAmbiguousLetters: 2 + clonesWithAmbiguousLetters: 1 clonesWithAmbiguousLettersInSplittingRegion: 0 - readsWithAmbiguousLetters: 2783.0 + readsWithAmbiguousLetters: 1351.0 readsWithAmbiguousLettersInSplittingRegion: 0.0 - totalAmbiguousLetters: 10 + totalAmbiguousLetters: 5 totalAmbiguousLettersInSplittingRegion: 0 initialCloneCount: 7 canceledAssemblies: 0 cloneBeforeFilteringCount: 7 finalCloneCount: 7 combinedCloneCount: 0 - totalReadsProcessed: 14107.0 + totalReadsProcessed: 13334.0 clonesClustered: 0 readsClustered: 0.0 - longestContigLength: 542 + longestContigLength: 541 totalDividedVariantReads: 0.0 assemblePrematureTerminationEvents: 0.0 assemblePartial: @@ -264,21 +254,21 @@ assemblePartial: - baseSingleCell.raw.refined.vdjca outputFiles: - baseSingleCell.raw.passembled.1.vdjca - independentRuns: 62 - totalProcessed: 28166 - outputAlignments: 28024 - withCDR3: 794 - overlapped: 142 - leftTooShortNRegion: 538 - kMerDiversity: 2270 + independentRuns: 61 + totalProcessed: 27637 + outputAlignments: 27498 + withCDR3: 765 + overlapped: 139 + leftTooShortNRegion: 523 + kMerDiversity: 2256 droppedWildcardsInKMer: 0 - droppedSmallOverlapNRegion: 125 + droppedSmallOverlapNRegion: 120 droppedNoNRegion: 0 - leftParts: 399 - rightParts: 9043 + leftParts: 393 + rightParts: 8861 complexOverlaps: 0 overOverlaps: 0 - partialAlignmentsAsIs: 27088 + partialAlignmentsAsIs: 26594 extend: type: extenderReport commandLine: extend -f --report baseSingleCell.raw.extend.report.txt --json-report @@ -287,15 +277,15 @@ extend: - baseSingleCell.raw.passembled.1.vdjca outputFiles: - baseSingleCell.raw.extended.vdjca - totalProcessed: 28024 - totalExtended: 26 + totalProcessed: 27498 + totalExtended: 24 vExtended: 8 vExtendedMerged: 0 - jExtended: 18 + jExtended: 16 jExtendedMerged: 0 vjExtended: 0 meanVExtensionLength: 1.0 - meanJExtensionLength: 3.111111111111111 + meanJExtensionLength: 3.125 refineTagsAndSort: type: refineTagsAndSort commandLine: refineTagsAndSort -f --report baseSingleCell.raw.refine.report.txt @@ -305,37 +295,37 @@ refineTagsAndSort: outputFiles: - baseSingleCell.raw.refined.vdjca correctionReport: - inputRecords: 40525 - outputRecords: 28166 + inputRecords: 40733 + outputRecords: 27637 steps: - tagName: CELL inputGroups: 1 - inputDiversity: 164 - inputCount: 40525 + inputDiversity: 165 + inputCount: 40733 coreDiversity: 84 - coreCount: 40443 - directlyCorrectedDiversity: 161 - directlyCorrectedCount: 795 + coreCount: 40650 + directlyCorrectedDiversity: 162 + directlyCorrectedCount: 798 filteredDiversity: 0 filteredCount: 0 recursivelyCorrected: 98 diversityFilteredByWhitelist: 0 outputDiversity: 3 - outputCount: 40525 + outputCount: 40733 - tagName: UMI inputGroups: 3 - inputDiversity: 424 - inputCount: 40525 - coreDiversity: 202 - coreCount: 40303 - directlyCorrectedDiversity: 315 - directlyCorrectedCount: 371 + inputDiversity: 418 + inputCount: 40733 + coreDiversity: 198 + coreCount: 40513 + directlyCorrectedDiversity: 313 + directlyCorrectedCount: 370 filteredDiversity: 1 filteredCount: 1 recursivelyCorrected: 15 diversityFilteredByWhitelist: 0 - outputDiversity: 108 - outputCount: 40524 + outputDiversity: 104 + outputCount: 40732 filterReport: type: and_report nestedReports: @@ -343,28 +333,28 @@ refineTagsAndSort: groupingKeys: - allTags:Cell - allTags:Molecule - numberOfGroups: 108 + numberOfGroups: 104 numberOfGroupsAccepted: 89 - totalWeight: 40524.0 - totalWeightAccepted: 40465.0 + totalWeight: 40732.0 + totalWeightAccepted: 40679.0 operatorReports: - operatorReport: type: multi_operator_hist_report - threshold: 25.0 + threshold: 24.0 nestedThresholds: - - 25.0 + - 24.0 - 413.0 metricHists: - bins: - from: 1.0 to: 1.5848931924611136 - weight: 12.0 + weight: 9.0 - from: 1.5848931924611136 to: 2.51188643150958 weight: 1.0 - from: 2.51188643150958 to: 3.981071705534973 - weight: 1.0 + weight: 0.0 - from: 3.981071705534973 to: 6.309573444801933 weight: 2.0 @@ -411,8 +401,8 @@ refineTagsAndSort: - allTags:Cell numberOfGroups: 3 numberOfGroupsAccepted: 3 - totalWeight: 40465.0 - totalWeightAccepted: 40465.0 + totalWeight: 40679.0 + totalWeightAccepted: 40679.0 operatorReports: - operatorReport: type: generic_hist_report @@ -444,133 +434,133 @@ refineTagsAndSort: - allTags:Cell - allTags:Molecule numberOfGroups: 89 - numberOfGroupsAccepted: 62 - totalWeight: 40465.0 - totalWeightAccepted: 28166.0 + numberOfGroupsAccepted: 61 + totalWeight: 40679.0 + totalWeightAccepted: 27637.0 operatorReports: - operatorReport: type: dummy_report metricHists: - bins: - - from: 56.0 - to: 62.0 + - from: 55.0 + to: 61.0 weight: 25.0 - - from: 62.0 - to: 68.0 + - from: 61.0 + to: 67.0 weight: 1.0 - - from: 68.0 - to: 74.0 + - from: 67.0 + to: 73.0 weight: 1.0 - - from: 74.0 - to: 80.0 + - from: 73.0 + to: 79.0 weight: 0.0 - - from: 80.0 - to: 86.0 + - from: 79.0 + to: 85.0 weight: 0.0 - - from: 86.0 - to: 92.0 + - from: 85.0 + to: 91.0 weight: 0.0 - - from: 92.0 - to: 98.0 + - from: 91.0 + to: 97.0 weight: 0.0 - - from: 98.0 - to: 104.0 + - from: 97.0 + to: 103.0 weight: 0.0 - - from: 104.0 - to: 110.0 + - from: 103.0 + to: 109.0 weight: 0.0 - - from: 110.0 - to: 116.0 + - from: 109.0 + to: 115.0 weight: 0.0 - - from: 116.0 - to: 122.0 + - from: 115.0 + to: 121.0 weight: 0.0 - - from: 122.0 - to: 128.0 + - from: 121.0 + to: 127.0 weight: 0.0 - - from: 128.0 - to: 134.0 + - from: 127.0 + to: 133.0 weight: 0.0 - - from: 134.0 - to: 140.0 + - from: 133.0 + to: 139.0 weight: 0.0 - - from: 140.0 - to: 146.0 + - from: 139.0 + to: 145.0 weight: 0.0 - - from: 146.0 - to: 152.0 - weight: 0.0 - - from: 152.0 - to: 158.0 + - from: 145.0 + to: 151.0 weight: 1.0 - - from: 158.0 - to: 164.0 + - from: 151.0 + to: 157.0 weight: 0.0 - - from: 164.0 - to: 170.0 + - from: 157.0 + to: 163.0 weight: 0.0 - - from: 170.0 - to: 176.0 + - from: 163.0 + to: 169.0 weight: 0.0 - - from: 176.0 - to: 182.0 - weight: 1.0 - - from: 182.0 - to: 188.0 + - from: 169.0 + to: 175.0 weight: 0.0 - - from: 188.0 - to: 194.0 + - from: 175.0 + to: 181.0 + weight: 1.0 + - from: 181.0 + to: 187.0 weight: 0.0 - - from: 194.0 - to: 200.0 + - from: 187.0 + to: 193.0 weight: 0.0 - - from: 200.0 - to: 206.0 + - from: 193.0 + to: 199.0 weight: 0.0 - - from: 206.0 - to: 212.0 + - from: 199.0 + to: 205.0 weight: 0.0 - - from: 212.0 - to: 218.0 - weight: 3.0 - - from: 218.0 - to: 224.0 + - from: 205.0 + to: 211.0 weight: 2.0 - - from: 224.0 - to: 230.0 + - from: 211.0 + to: 217.0 + weight: 1.0 + - from: 217.0 + to: 223.0 weight: 2.0 - - from: 230.0 - to: 236.0 - weight: 8.0 - - from: 236.0 - to: 242.0 - weight: 10.0 - - from: 242.0 - to: 248.0 - weight: 8.0 - - from: 248.0 - to: 254.0 - weight: 12.0 - - from: 254.0 - to: 260.0 - weight: 7.0 - - from: 260.0 - to: 266.0 + - from: 223.0 + to: 229.0 + weight: 3.0 + - from: 229.0 + to: 235.0 weight: 6.0 - - from: 266.0 - to: 272.0 + - from: 235.0 + to: 241.0 + weight: 9.0 + - from: 241.0 + to: 247.0 + weight: 7.0 + - from: 247.0 + to: 253.0 + weight: 13.0 + - from: 253.0 + to: 259.0 + weight: 10.0 + - from: 259.0 + to: 265.0 + weight: 5.0 + - from: 265.0 + to: 271.0 weight: 1.0 - - from: 272.0 - to: 278.0 + - from: 271.0 + to: 277.0 weight: 0.0 - - from: 278.0 - to: 284.0 + - from: 277.0 + to: 283.0 weight: 0.0 - - from: 284.0 - to: 290.0 + - from: 283.0 + to: 289.0 weight: 0.0 - - from: 290.0 - to: 296.0 + - from: 289.0 + to: 295.0 weight: 1.0 collectionSpec: log: false diff --git a/regression/reports/baseSingleCell.vdjcontigs.yaml b/regression/reports/baseSingleCell.vdjcontigs.yaml index 26e213420..d4cae3684 100644 --- a/regression/reports/baseSingleCell.vdjcontigs.yaml +++ b/regression/reports/baseSingleCell.vdjcontigs.yaml @@ -10,24 +10,24 @@ align: outputFiles: - baseSingleCell.vdjcontigs.vdjca totalReadsProcessed: 46879 - aligned: 40525 - notAligned: 6354 + aligned: 40733 + notAligned: 6146 notAlignedReasons: - NoHits: 5776 + NoHits: 6094 FailedAfterAOverlap: 0 NoCDR3Parts: 0 NoVHits: 0 NoJHits: 0 VAndJOnDifferentTargets: 0 - LowTotalScore: 578 + LowTotalScore: 52 NoBarcode: 0 SampleNotMatched: 0 overlapped: 0 overlappedAligned: 0 overlappedNotAligned: 0 alignmentAidedOverlaps: 0 - noCDR3PartsAlignments: 17724 - partialAlignments: 22009 + noCDR3PartsAlignments: 17643 + partialAlignments: 22298 chimeras: 0 vChimeras: 0 jChimeras: 0 @@ -38,40 +38,30 @@ align: chainUsage: type: chainUsage chimeras: 0 - total: 40525 + total: 40733 chains: - IGH: - total: 21 - nonFunctional: 0 - isOOF: 0 - hasStops: 0 - IGK: - total: 17 - nonFunctional: 0 - isOOF: 0 - hasStops: 0 IGL: - total: 15 + total: 2 nonFunctional: 0 isOOF: 0 hasStops: 0 TRA: - total: 2589 + total: 2845 nonFunctional: 27 isOOF: 27 hasStops: 0 TRAD: - total: 2980 + total: 2970 nonFunctional: 0 isOOF: 0 hasStops: 0 TRB: - total: 34901 + total: 34915 nonFunctional: 3 isOOF: 1 hasStops: 2 TRG: - total: 2 + total: 1 nonFunctional: 0 isOOF: 0 hasStops: 0 @@ -150,8 +140,8 @@ assemble: type: preCloneAssemblerReport inputGroups: 3 groupsWithNoAssemblingFeature: 0 - inputAlignments: 28024 - inputAlignmentsWithAssemblingFeature: 936 + inputAlignments: 27498 + inputAlignmentsWithAssemblingFeature: 904 coreAlignmentsDroppedByUncertainChain: 0 corePreClonesDroppedByTagSuffix: 0 coreAlignmentsDroppedByTagSuffix: 0 @@ -160,38 +150,38 @@ assemble: "2": 1 "3": 2 assemblingFeatureSequencesInZeroPreClones: 0 - coreAlignments: 857 + coreAlignments: 825 tagConflicts: 1 geneAndTagConflicts: 1 geneConflicts: Variable: 1 discardedCoreAlignments: 79 - empiricallyAssignedAlignments: 13109 - vjEmpiricallyAssignedAlignments: 8 + empiricallyAssignedAlignments: 12371 + vjEmpiricallyAssignedAlignments: 10 tagEmpiricallyAssignedAlignments: 0 - geneAndTagEmpiricallyAssignedAlignments: 13101 + geneAndTagEmpiricallyAssignedAlignments: 12361 empiricalAssignmentConflicts: 0 ignoredAlignments: 0 - unassignedAlignments: 14058 - totalReadsProcessed: 46737 + unassignedAlignments: 14302 + totalReadsProcessed: 46740 totalAlignmentsProcessed: 8 - totalAlignedReadsProcessed: 14108 - initialClonesCreated: 7 - readsDroppedNoTargetSequence: 27088 + totalAlignedReadsProcessed: 13335 + initialClonesCreated: 8 + readsDroppedNoTargetSequence: 26594 readsDroppedTooShortClonalSequence: 0 readsDroppedLowQuality: 0 - coreReads: 14107 - readsDroppedFailedMapping: 1 + coreReads: 13334 + readsDroppedFailedMapping: 0 lowQualityRescued: 0 clonesClustered: 0 readsClustered: 0 clones: 7 - clonesDroppedAsLowQuality: 0 + clonesDroppedAsLowQuality: 1 clonesPreClustered: 0 readsPreClustered: 0 - readsInClones: 14107 - readsInClonesBeforeClustering: 14107 - readsDroppedWithLowQualityClones: 0 + readsInClones: 13334 + readsInClonesBeforeClustering: 13334 + readsDroppedWithLowQualityClones: 1 clonalChainUsage: type: chainUsage chimeras: 0 @@ -220,8 +210,8 @@ assemble: - allTags:Cell numberOfGroups: 7 numberOfGroupsAccepted: 7 - totalWeight: 14107.0 - totalWeightAccepted: 14107.0 + totalWeight: 13334.0 + totalWeightAccepted: 13334.0 operatorReports: - operatorReport: type: generic_hist_report @@ -250,7 +240,7 @@ assembleContigs: cloneBeforeFilteringCount: 7 finalCloneCount: 6 combinedCloneCount: 0 - totalReadsProcessed: 14107.0 + totalReadsProcessed: 13334.0 clonesClustered: 0 readsClustered: 0.0 longestContigLength: 349 @@ -265,21 +255,21 @@ assemblePartial: - baseSingleCell.vdjcontigs.refined.vdjca outputFiles: - baseSingleCell.vdjcontigs.passembled.1.vdjca - independentRuns: 62 - totalProcessed: 28166 - outputAlignments: 28024 - withCDR3: 794 - overlapped: 142 - leftTooShortNRegion: 538 - kMerDiversity: 2270 + independentRuns: 61 + totalProcessed: 27637 + outputAlignments: 27498 + withCDR3: 765 + overlapped: 139 + leftTooShortNRegion: 523 + kMerDiversity: 2256 droppedWildcardsInKMer: 0 - droppedSmallOverlapNRegion: 125 + droppedSmallOverlapNRegion: 120 droppedNoNRegion: 0 - leftParts: 399 - rightParts: 9043 + leftParts: 393 + rightParts: 8861 complexOverlaps: 0 overOverlaps: 0 - partialAlignmentsAsIs: 27088 + partialAlignmentsAsIs: 26594 extend: type: extenderReport commandLine: extend -f --report baseSingleCell.vdjcontigs.extend.report.txt --json-report @@ -289,15 +279,15 @@ extend: - baseSingleCell.vdjcontigs.passembled.1.vdjca outputFiles: - baseSingleCell.vdjcontigs.extended.vdjca - totalProcessed: 28024 - totalExtended: 26 + totalProcessed: 27498 + totalExtended: 24 vExtended: 8 vExtendedMerged: 0 - jExtended: 18 + jExtended: 16 jExtendedMerged: 0 vjExtended: 0 meanVExtensionLength: 1.0 - meanJExtensionLength: 3.111111111111111 + meanJExtensionLength: 3.125 refineTagsAndSort: type: refineTagsAndSort commandLine: refineTagsAndSort -f --report baseSingleCell.vdjcontigs.refine.report.txt @@ -308,37 +298,37 @@ refineTagsAndSort: outputFiles: - baseSingleCell.vdjcontigs.refined.vdjca correctionReport: - inputRecords: 40525 - outputRecords: 28166 + inputRecords: 40733 + outputRecords: 27637 steps: - tagName: CELL inputGroups: 1 - inputDiversity: 164 - inputCount: 40525 + inputDiversity: 165 + inputCount: 40733 coreDiversity: 84 - coreCount: 40443 - directlyCorrectedDiversity: 161 - directlyCorrectedCount: 795 + coreCount: 40650 + directlyCorrectedDiversity: 162 + directlyCorrectedCount: 798 filteredDiversity: 0 filteredCount: 0 recursivelyCorrected: 98 diversityFilteredByWhitelist: 0 outputDiversity: 3 - outputCount: 40525 + outputCount: 40733 - tagName: UMI inputGroups: 3 - inputDiversity: 424 - inputCount: 40525 - coreDiversity: 202 - coreCount: 40303 - directlyCorrectedDiversity: 315 - directlyCorrectedCount: 371 + inputDiversity: 418 + inputCount: 40733 + coreDiversity: 198 + coreCount: 40513 + directlyCorrectedDiversity: 313 + directlyCorrectedCount: 370 filteredDiversity: 1 filteredCount: 1 recursivelyCorrected: 15 diversityFilteredByWhitelist: 0 - outputDiversity: 108 - outputCount: 40524 + outputDiversity: 104 + outputCount: 40732 filterReport: type: and_report nestedReports: @@ -346,28 +336,28 @@ refineTagsAndSort: groupingKeys: - allTags:Cell - allTags:Molecule - numberOfGroups: 108 + numberOfGroups: 104 numberOfGroupsAccepted: 89 - totalWeight: 40524.0 - totalWeightAccepted: 40465.0 + totalWeight: 40732.0 + totalWeightAccepted: 40679.0 operatorReports: - operatorReport: type: multi_operator_hist_report - threshold: 25.0 + threshold: 24.0 nestedThresholds: - - 25.0 + - 24.0 - 413.0 metricHists: - bins: - from: 1.0 to: 1.5848931924611136 - weight: 12.0 + weight: 9.0 - from: 1.5848931924611136 to: 2.51188643150958 weight: 1.0 - from: 2.51188643150958 to: 3.981071705534973 - weight: 1.0 + weight: 0.0 - from: 3.981071705534973 to: 6.309573444801933 weight: 2.0 @@ -414,8 +404,8 @@ refineTagsAndSort: - allTags:Cell numberOfGroups: 3 numberOfGroupsAccepted: 3 - totalWeight: 40465.0 - totalWeightAccepted: 40465.0 + totalWeight: 40679.0 + totalWeightAccepted: 40679.0 operatorReports: - operatorReport: type: generic_hist_report @@ -447,133 +437,133 @@ refineTagsAndSort: - allTags:Cell - allTags:Molecule numberOfGroups: 89 - numberOfGroupsAccepted: 62 - totalWeight: 40465.0 - totalWeightAccepted: 28166.0 + numberOfGroupsAccepted: 61 + totalWeight: 40679.0 + totalWeightAccepted: 27637.0 operatorReports: - operatorReport: type: dummy_report metricHists: - bins: - - from: 56.0 - to: 62.0 + - from: 55.0 + to: 61.0 weight: 25.0 - - from: 62.0 - to: 68.0 + - from: 61.0 + to: 67.0 weight: 1.0 - - from: 68.0 - to: 74.0 + - from: 67.0 + to: 73.0 weight: 1.0 - - from: 74.0 - to: 80.0 + - from: 73.0 + to: 79.0 weight: 0.0 - - from: 80.0 - to: 86.0 + - from: 79.0 + to: 85.0 weight: 0.0 - - from: 86.0 - to: 92.0 + - from: 85.0 + to: 91.0 weight: 0.0 - - from: 92.0 - to: 98.0 + - from: 91.0 + to: 97.0 weight: 0.0 - - from: 98.0 - to: 104.0 + - from: 97.0 + to: 103.0 weight: 0.0 - - from: 104.0 - to: 110.0 + - from: 103.0 + to: 109.0 weight: 0.0 - - from: 110.0 - to: 116.0 + - from: 109.0 + to: 115.0 weight: 0.0 - - from: 116.0 - to: 122.0 + - from: 115.0 + to: 121.0 weight: 0.0 - - from: 122.0 - to: 128.0 + - from: 121.0 + to: 127.0 weight: 0.0 - - from: 128.0 - to: 134.0 + - from: 127.0 + to: 133.0 weight: 0.0 - - from: 134.0 - to: 140.0 + - from: 133.0 + to: 139.0 weight: 0.0 - - from: 140.0 - to: 146.0 + - from: 139.0 + to: 145.0 weight: 0.0 - - from: 146.0 - to: 152.0 - weight: 0.0 - - from: 152.0 - to: 158.0 + - from: 145.0 + to: 151.0 weight: 1.0 - - from: 158.0 - to: 164.0 + - from: 151.0 + to: 157.0 weight: 0.0 - - from: 164.0 - to: 170.0 + - from: 157.0 + to: 163.0 weight: 0.0 - - from: 170.0 - to: 176.0 + - from: 163.0 + to: 169.0 weight: 0.0 - - from: 176.0 - to: 182.0 - weight: 1.0 - - from: 182.0 - to: 188.0 + - from: 169.0 + to: 175.0 weight: 0.0 - - from: 188.0 - to: 194.0 + - from: 175.0 + to: 181.0 + weight: 1.0 + - from: 181.0 + to: 187.0 weight: 0.0 - - from: 194.0 - to: 200.0 + - from: 187.0 + to: 193.0 weight: 0.0 - - from: 200.0 - to: 206.0 + - from: 193.0 + to: 199.0 weight: 0.0 - - from: 206.0 - to: 212.0 + - from: 199.0 + to: 205.0 weight: 0.0 - - from: 212.0 - to: 218.0 - weight: 3.0 - - from: 218.0 - to: 224.0 + - from: 205.0 + to: 211.0 weight: 2.0 - - from: 224.0 - to: 230.0 + - from: 211.0 + to: 217.0 + weight: 1.0 + - from: 217.0 + to: 223.0 weight: 2.0 - - from: 230.0 - to: 236.0 - weight: 8.0 - - from: 236.0 - to: 242.0 - weight: 10.0 - - from: 242.0 - to: 248.0 - weight: 8.0 - - from: 248.0 - to: 254.0 - weight: 12.0 - - from: 254.0 - to: 260.0 - weight: 7.0 - - from: 260.0 - to: 266.0 + - from: 223.0 + to: 229.0 + weight: 3.0 + - from: 229.0 + to: 235.0 weight: 6.0 - - from: 266.0 - to: 272.0 + - from: 235.0 + to: 241.0 + weight: 9.0 + - from: 241.0 + to: 247.0 + weight: 7.0 + - from: 247.0 + to: 253.0 + weight: 13.0 + - from: 253.0 + to: 259.0 + weight: 10.0 + - from: 259.0 + to: 265.0 + weight: 5.0 + - from: 265.0 + to: 271.0 weight: 1.0 - - from: 272.0 - to: 278.0 + - from: 271.0 + to: 277.0 weight: 0.0 - - from: 278.0 - to: 284.0 + - from: 277.0 + to: 283.0 weight: 0.0 - - from: 284.0 - to: 290.0 + - from: 283.0 + to: 289.0 weight: 0.0 - - from: 290.0 - to: 296.0 + - from: 289.0 + to: 295.0 weight: 1.0 collectionSpec: log: false