Merge pull request #1740 from milaboratory/mixcr-regression-tests/4-7…

…-0-RC-plus-mitool-integration Regression tests changes in the 4-7-0-RC-plus-mitool-integration
milaboratory · Aug 7, 2024 · 0f7f626 · 0f7f626
2 parents fee97d3 + 6ed9c33
commit 0f7f626
Show file tree

Hide file tree

Showing 4 changed files with 100 additions and 0 deletions.
diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-1-1-1.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-1-1-1.yaml
@@ -157,6 +157,7 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    retriesForPartialAlignments: 3
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true
@@ -259,6 +260,14 @@ assemble:
       maxConsensuses: 3
     minTagSuffixShare: 0.0
     isolateChains: false
+    empiricalAlignmentAssignment:
+      uniqGeneOccurrenceWithinTag:
+        - V
+        - J
+      uniqGeneOccurrenceWithinCluster:
+        - V
+        - J
+      matchAlignmentsWithoutVJHitsByTags: true
   cloneAssemblerParameters:
     assemblingFeatures:
       - CDR3
@@ -323,6 +332,22 @@ 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
 exportAlignments:
   chains: ALL
   noHeader: false

diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-16-4-1.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-16-4-1.yaml
@@ -157,6 +157,7 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    retriesForPartialAlignments: 3
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true
@@ -259,6 +260,14 @@ assemble:
       maxConsensuses: 3
     minTagSuffixShare: 0.0
     isolateChains: false
+    empiricalAlignmentAssignment:
+      uniqGeneOccurrenceWithinTag:
+        - V
+        - J
+      uniqGeneOccurrenceWithinCluster:
+        - V
+        - J
+      matchAlignmentsWithoutVJHitsByTags: true
   cloneAssemblerParameters:
     assemblingFeatures:
       - CDR3
@@ -323,6 +332,22 @@ 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
 exportAlignments:
   chains: ALL
   noHeader: false

diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-1-1-1.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-1-1-1.yaml
@@ -157,6 +157,7 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    retriesForPartialAlignments: 3
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true
@@ -259,6 +260,14 @@ assemble:
       maxConsensuses: 3
     minTagSuffixShare: 0.0
     isolateChains: false
+    empiricalAlignmentAssignment:
+      uniqGeneOccurrenceWithinTag:
+        - V
+        - J
+      uniqGeneOccurrenceWithinCluster:
+        - V
+        - J
+      matchAlignmentsWithoutVJHitsByTags: true
   cloneAssemblerParameters:
     assemblingFeatures:
       - CDR3
@@ -323,6 +332,22 @@ 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
 exportAlignments:
   chains: ALL
   noHeader: false

diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-16-4-1.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-16-4-1.yaml
@@ -157,6 +157,7 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    retriesForPartialAlignments: 3
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true
@@ -259,6 +260,14 @@ assemble:
       maxConsensuses: 3
     minTagSuffixShare: 0.0
     isolateChains: false
+    empiricalAlignmentAssignment:
+      uniqGeneOccurrenceWithinTag:
+        - V
+        - J
+      uniqGeneOccurrenceWithinCluster:
+        - V
+        - J
+      matchAlignmentsWithoutVJHitsByTags: true
   cloneAssemblerParameters:
     assemblingFeatures:
       - CDR3
@@ -323,6 +332,22 @@ 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
 exportAlignments:
   chains: ALL
   noHeader: false