diff --git a/build.gradle.kts b/build.gradle.kts index 8dabc2189..eb14c95a3 100644 --- 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 index 492e8db9d..f7b2eb912 100644 --- 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 index 92b5eefd8..6e459c9c2 100644 --- 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 index f5b82655d..881e960c8 100644 --- 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 index 4b899b755..5d786aaf5 100644 --- 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 index c400d98f2..66ac58814 100644 --- 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 index e59dadce7..809c4bc92 100644 --- 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 index 4b899b755..5d786aaf5 100644 --- 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 index 4b899b755..5d786aaf5 100644 --- 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 index e62fe180b..879d61acd 100644 --- 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 index 4d5bd54c5..918343bc9 100644 --- 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 index 1dc45bf13..dcd85d55f 100644 --- 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 \ No newline at end of file + smartForceEdgeAlignments: true diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java index cc2b3e89a..dd1fa8dae 100644 --- 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);