Merge pull request #1773 from milaboratory/align-retry

Align retry
milaboratory · Sep 16, 2024 · 1582589 · 1582589
2 parents 3956c95 + 14f978f
commit 1582589
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diff --git a/build.gradle.kts b/build.gradle.kts
@@ -134,7 +134,7 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.7.0-20-export-for-platforma"
+val mixcrAlgoVersion = "4.7.0-26-align-retry"
 // may be blank (will be inherited from mixcr-algo)
 val milibVersion = ""
 // may be blank (will be inherited from mixcr-algo or milib)

diff --git a/changelogs/v4.7.1.md b/changelogs/v4.7.1.md
@@ -1,8 +1,8 @@
 ## 🛠️ Other improvements & fixes
 
 - Tracking the progres of fasta[.gz] inputs on `align`.
-
+- Improved alignment rate of short parts of genes in reads with height rate of mutations
 
 ## 📚 New Presets
 
-- Added preset `bruker-human-sc-xcr-vdj-beacon` for TCR/BCR analyses of Bruker Beacon data  
+- Added preset `bruker-human-sc-xcr-vdj-beacon` for TCR/BCR analyses of Bruker Beacon data  
diff --git a/itests/case008.sh b/itests/case008.sh
@@ -29,10 +29,10 @@ mixcr analyze --verbose generic-amplicon \
   -Malign.parameters.readsLayout=Collinear \
   CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case8
 
-assert "cat case8.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241313"
-assert "cat case8.assemble.report.json | head -n 1 | jq -r .readsInClones" "200731"
-assert "cat case8.assemble.report.json | head -n 1 | jq -r .clones" "25653"
+assert "cat case8.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241364"
+assert "cat case8.assemble.report.json | head -n 1 | jq -r .readsInClones" "200784"
+assert "cat case8.assemble.report.json | head -n 1 | jq -r .clones" "25662"
 assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .longestContigLength" "499"
-assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3543"
+assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3547"
 assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .assemblePrematureTerminationEvents" "4"
-assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25653"
+assert "cat case8.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25662"
diff --git a/itests/case009.sh b/itests/case009.sh
@@ -30,9 +30,9 @@ mixcr analyze --verbose generic-amplicon \
   -M align.parameters.readsLayout=Collinear \
   CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case9
 
-assert "cat case9.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241313"
-assert "cat case9.assemble.report.json | head -n 1 | jq -r .readsInClones" "200731"
+assert "cat case9.align.report.json | head -n 1 | jq -r .chainUsage.chains.TRA.total" "241364"
+assert "cat case9.assemble.report.json | head -n 1 | jq -r .readsInClones" "200784"
 assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .longestContigLength" "499"
-assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3543"
+assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .clonesWithAmbiguousLetters" "3547"
 assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .assemblePrematureTerminationEvents" "4"
-assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25653"
+assert "cat case9.assembleContigs.report.json | head -n 1 | jq -r .finalCloneCount" "25662"
diff --git a/regression/presets/analyze/10x-5gex-cdr3.yaml b/regression/presets/analyze/10x-5gex-cdr3.yaml
@@ -167,6 +167,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists:
     CELL: builtin:737K-august-2016

diff --git a/regression/presets/analyze/10x-5gex-full-length.yaml b/regression/presets/analyze/10x-5gex-full-length.yaml
@@ -168,6 +168,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists:
     CELL: builtin:737K-august-2016

diff --git a/regression/presets/analyze/10x-sc-5gex.yaml b/regression/presets/analyze/10x-sc-5gex.yaml
@@ -167,6 +167,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists:
     CELL: builtin:737K-august-2016

diff --git a/regression/presets/analyze/10x-sc-xcr-vdj.yaml b/regression/presets/analyze/10x-sc-xcr-vdj.yaml
@@ -341,6 +341,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml
@@ -341,6 +341,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml
@@ -341,6 +341,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

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
@@ -341,6 +341,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml
@@ -341,6 +341,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml
@@ -162,6 +162,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml
@@ -343,6 +343,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/10x-vdj-tcr.yaml b/regression/presets/analyze/10x-vdj-tcr.yaml
@@ -341,6 +341,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml
@@ -155,6 +155,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/abhelix-human-bcr-full-length.yaml b/regression/presets/analyze/abhelix-human-bcr-full-length.yaml
@@ -155,6 +155,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/abhelix-human-rna-xcr.yaml b/regression/presets/analyze/abhelix-human-rna-xcr.yaml
@@ -155,6 +155,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml
@@ -155,6 +155,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/abhelix-human-tcr-full-length.yaml b/regression/presets/analyze/abhelix-human-tcr-full-length.yaml
@@ -155,6 +155,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml
@@ -127,6 +127,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml
@@ -127,6 +127,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml
@@ -127,6 +127,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml b/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml
@@ -808,6 +808,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml b/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml
@@ -813,6 +813,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml
@@ -801,6 +801,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml
@@ -808,6 +808,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml
@@ -808,6 +808,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml
@@ -801,6 +801,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml
@@ -808,6 +808,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml
@@ -808,6 +808,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml
@@ -801,6 +801,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml
@@ -813,6 +813,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml
@@ -813,6 +813,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml
@@ -801,6 +801,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml
@@ -813,6 +813,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml
@@ -813,6 +813,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

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
@@ -2529,6 +2529,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml
@@ -801,6 +801,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml b/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml
@@ -127,6 +127,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/biomed2-human-bcr-full-length.yaml b/regression/presets/analyze/biomed2-human-bcr-full-length.yaml
@@ -127,6 +127,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/biomed2-human-rna-igh.yaml b/regression/presets/analyze/biomed2-human-rna-igh.yaml
@@ -127,6 +127,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/biomed2-human-rna-igkl.yaml b/regression/presets/analyze/biomed2-human-rna-igkl.yaml
@@ -127,6 +127,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/biomed2-human-rna-trbdg.yaml b/regression/presets/analyze/biomed2-human-rna-trbdg.yaml
@@ -127,6 +127,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/bruker-human-sc-xcr-vdj-beacon.yaml b/regression/presets/analyze/bruker-human-sc-xcr-vdj-beacon.yaml
@@ -277,6 +277,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: false

diff --git a/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml
@@ -130,6 +130,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml
@@ -158,6 +158,7 @@ align:
     saveOriginalReads: false
     smartForceEdgeAlignments: true
     retriesForPartialAlignments: 3
+    retriesAlignmentOfNotCoveredPart: 2
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true