regression tests automated change

milaboratory · Apr 4, 2024 · 446dd87 · 446dd87
1 parent 5c11f91
commit 446dd87
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Showing 77 changed files with 1,106 additions and 525 deletions.
diff --git 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: 0.9
         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
@@ -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: 0.9
         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
@@ -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: 0.9
         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
@@ -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
@@ -432,6 +434,22 @@ 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
@@ -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
@@ -436,6 +437,22 @@ 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
@@ -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
@@ -432,6 +434,22 @@ 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