Merge pull request #1620 from milaboratory/fix-nanopore

Fix nanopore
milaboratory · Apr 23, 2024 · e929f89 · e929f89
2 parents 88d34d8 + 62beb1e
commit e929f89
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Showing 13 changed files with 30 additions and 3 deletions.
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 = "4.6.0-93-feature-imputed"
+val mixcrAlgoVersion = "4.6.0-99-fix-nanopore"
 // 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/v4.6.1.md b/changelogs/v4.6.1.md
@@ -36,6 +36,7 @@
 - Fixed calculation of germline for `VCDR3Part` and `JCDR3Part` in case of indels inside CDR3
 - Fixed export of trees if data assembled by a feature with reference point having offset
 - Export of `VJJunction gemline` in `shmTrees` exports now export `mrca` as most plausible content
+- Fixed parsing and alignment of reads with length more than 30Kbase
 
 ## New Presets
 

diff --git a/regression/presets/analyze/flairr-seq-bcr.yaml b/regression/presets/analyze/flairr-seq-bcr.yaml
@@ -158,6 +158,8 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    longReadsParameters:
+      windowSize: 1500
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/generic-ont-with-umi.yaml b/regression/presets/analyze/generic-ont-with-umi.yaml
@@ -160,6 +160,8 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    longReadsParameters:
+      windowSize: 1500
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/generic-ont.yaml b/regression/presets/analyze/generic-ont.yaml
@@ -156,6 +156,8 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    longReadsParameters:
+      windowSize: 1500
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/generic-pacbio-with-umi.yaml b/regression/presets/analyze/generic-pacbio-with-umi.yaml
@@ -159,6 +159,8 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    longReadsParameters:
+      windowSize: 1500
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/generic-pacbio.yaml b/regression/presets/analyze/generic-pacbio.yaml
@@ -155,6 +155,8 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    longReadsParameters:
+      windowSize: 1500
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml b/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml
@@ -156,6 +156,8 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    longReadsParameters:
+      windowSize: 1500
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/presets/analyze/ont-rna-seq.yaml b/regression/presets/analyze/ont-rna-seq.yaml
@@ -156,6 +156,8 @@ align:
     saveOriginalSequence: false
     saveOriginalReads: false
     smartForceEdgeAlignments: true
+    longReadsParameters:
+      windowSize: 1500
 refineTagsAndSort:
   whitelists: {}
   runCorrection: true

diff --git a/regression/schemas/analyzeBundle/parameters/align.schema.yaml b/regression/schemas/analyzeBundle/parameters/align.schema.yaml
@@ -217,6 +217,11 @@ properties:
         enum:
           - Unknown
           - R1V
+      longReadsParameters:
+        type: object
+        properties:
+          windowSize:
+            type: integer
       mergerParameters:
         type: object
         properties:

diff --git a/regression/schemas/parametersForOverride/VDJCAlignerParameters.schema.yaml b/regression/schemas/parametersForOverride/VDJCAlignerParameters.schema.yaml
@@ -30,6 +30,11 @@ properties:
     enum:
       - Unknown
       - R1V
+  longReadsParameters:
+    type: object
+    properties:
+      windowSize:
+        type: integer
   mergerParameters:
     type: object
     properties:

diff --git a/src/main/resources/presets/blocks/01-align.yaml b/src/main/resources/presets/blocks/01-align.yaml
@@ -289,6 +289,8 @@ align-long-read:
     #   - type: MustNotContainTagType
     #     tagType: Sample
     parameters:
+      longReadsParameters:
+        windowSize: 1500
       vParameters:
         geneFeatureToAlign: VTranscriptWithP
         minSumScore: 150
@@ -566,4 +568,4 @@ align-single-cell:
       minChimeraDetectionScore: 120
       vjOverlapWindow: 3
       saveOriginalReads: false
-      smartForceEdgeAlignments: true
+      smartForceEdgeAlignments: true
diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java
@@ -45,7 +45,7 @@ public void test1() throws Exception {
                 VJAlignmentOrder.JThenV, VDJCLibraryStructure.Unknown,
                 false, false,
                 120.0f, 0, 0.7f, false, false, false, PairedEndReadsLayout.Opposite, new MergerParameters(
-                QualityMergingAlgorithm.SumSubtraction, null, 12, 12, null, 0.12, Unweighted), false, 5, 120, 10, true, true, true);
+                QualityMergingAlgorithm.SumSubtraction, null, 12, 12, null, 0.12, Unweighted), false, 5, 120, 10, true, true, true, null);
 
         String str = GlobalObjectMappers.getPretty().writeValueAsString(paramentrs);
         VDJCAlignerParameters deser = GlobalObjectMappers.getPretty().readValue(str, VDJCAlignerParameters.class);