From 7f6779c69c6821bd0a4e454d5747e53a9b5b0438 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Mon, 26 Jun 2023 13:39:37 +0200 Subject: [PATCH 01/15] refactoring of getTagDiversity --- .../milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt | 4 ++-- .../kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt | 2 +- .../com/milaboratory/mixcr/cli/CommandExportClonesPretty.kt | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt index 5f1f44c2d..2c2d78c1c 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt @@ -356,8 +356,8 @@ class CommandExportAlignmentsPretty : MiXCRCommandWithOutputs() { println() println(">>> Tags:") tagsInfo.forEach { tag -> - val tagValue = alignments.tagCount.singleOrNull(tag.index).extractKey() - val toPrint = tagValue.extractSequence() ?: tagValue.toString() + val tagValue = alignments.tagCount.singleOrNull(tag)?.extractKey() + val toPrint = tagValue?.extractSequence() ?: tagValue.toString() println(">>> ${tag.name}: $toPrint") } } diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt index b294aebdd..1a334ae3e 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt @@ -373,7 +373,7 @@ object CommandExportClones { private class CloneTagGroupingKey(private val tagIdx: Int) : CloneGroupingKey { override fun getLabel(clone: Clone): String = - clone.tagFractions!!.asKeyPrefixOrError(tagIdx + 1).get(tagIdx).toString() + clone.tagCount.asKeyPrefixOrError(tagIdx + 1).get(tagIdx).toString() } private fun parseGroupingKey(header: MiXCRHeader, key: String) = diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClonesPretty.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClonesPretty.kt index 5c98fb0ac..18b6771be 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClonesPretty.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClonesPretty.kt @@ -189,7 +189,7 @@ class CommandExportClonesPretty : MiXCRCommandWithOutputs() { if (tagsInfo != TagsInfo.NO_TAGS) { println(">>> Tags:") tagsInfo.forEach { tag -> - output.println(">>> ${tag.name}: ${clone.tagCount.getTagDiversity(tag.index + 1)}") + output.println(">>> ${tag.name}: ${clone.getTagDiversity(tag)}") } } output.println() From a750686e73919fcd0542cb75a680fffba1b75d88 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Mon, 26 Jun 2023 14:10:07 +0200 Subject: [PATCH 02/15] update version --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 185c8b5d2..381bd4b87 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -130,7 +130,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.3.0-201-precalculate_fraction" +val mixcrAlgoVersion = "4.3.0-203-tiny-things" val milibVersion = "" val mitoolVersion = "" val repseqioVersion = "1.8.0-77-master" From 390457cd2e95971d96f55e10aa35cb99152f9c8d Mon Sep 17 00:00:00 2001 From: gnefedev Date: Mon, 26 Jun 2023 14:14:19 +0200 Subject: [PATCH 03/15] add default export of readIds --- src/main/resources/presets/blocks/03-exportAlignments.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/resources/presets/blocks/03-exportAlignments.yaml b/src/main/resources/presets/blocks/03-exportAlignments.yaml index 724af4660..4e88c6318 100644 --- a/src/main/resources/presets/blocks/03-exportAlignments.yaml +++ b/src/main/resources/presets/blocks/03-exportAlignments.yaml @@ -3,6 +3,7 @@ exportAlignments-base: exportAlignments: chains: ALL fields: + - field: "-readIds" - field: "-targetSequences" - field: "-targetQualities" - field: "-vHitsWithScore" From f95200cdb512d42f0ae4e7e31d7a1c747859ef32 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Mon, 26 Jun 2023 14:46:27 +0200 Subject: [PATCH 04/15] changelog --- changelogs/v4.4.md | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/changelogs/v4.4.md b/changelogs/v4.4.md index ade2cdedb..83fb470a8 100644 --- a/changelogs/v4.4.md +++ b/changelogs/v4.4.md @@ -35,16 +35,27 @@ - added gene feature coverage in alignment report - on Linux platforms default calculation of -Xmx now based on "available" memory (previously "free" was used) - new gene aligner parameter `edgeRealignmentMinScoreOverride` for more sensitive alignments for short paired-end reads -- report values downstream `align` now calculate percents relative to the number of reads in the sample rather than the total number of reads in multi-sample analysis -- options helping with advanced analysis of data quality and consensus assembly process added to `assemble` (`--consensus-alignments`, `--consensus-state-stat`, `--downsample-consensus-state-stat`) and `analyze` (`--output-consensus-alignments`, `--output-consensus-state-stat`, `--downsample-consensus-state-stat`) +- report values downstream `align` now calculate percents relative to the number of reads in the sample rather than the + total number of reads in multi-sample analysis +- options helping with advanced analysis of data quality and consensus assembly process added + to `assemble` (`--consensus-alignments`, `--consensus-state-stat`, `--downsample-consensus-state-stat`) + and `analyze` (`--output-consensus-alignments`, `--output-consensus-state-stat`, `--downsample-consensus-state-stat`) - fixed bug not allowing to parse more than two reads with tag pattern - better tag pattern search projection representation in reports - fix for value in report line `Reads dropped due to low quality, percent of total report string` - additional report string "Aligned reads processed" in `assemble` report -- fix bug when `--chains` is used with `exportClonesOverlap` +- fix bug when `--chains` is used with `exportClonesOverlap` - fix for `export...` - tag quality field added back to export columns - fixes bug not allowing to use more than 2 input reads in pattern matching -- add options `--by-feature` and `--by-gene` to `sortClones` +- added options `--by-feature` and `--by-gene` to `sortClones` +- added options `-rankByReads` and `-rankByTag <(Molecule|Cell|Sample)>` to `exportClones` + and `exportShmTreesWithNodes.txt` +- export readIds in `exportAlignments` by default +- `findAlleles` now recalculate functionality of de novo found alleles +- add info about CDR3 in generated hash for de novo alleles +- more robust algorithm for calculating checksum of library +- remove de novo alleles that are actually the same, will be left only one +- `findAlleles` will remove not used genes from library (genes that not represented in given donor) ## Braking changes From 6033374643562cad0353e8d1f1d04e1732064ca9 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Mon, 26 Jun 2023 15:19:50 +0000 Subject: [PATCH 05/15] regression tests automated change --- regression/presets/analyze/10x-5gex-cdr3.yaml | 1 + regression/presets/analyze/10x-5gex-full-length.yaml | 1 + regression/presets/analyze/10x-5gex.yaml | 1 + regression/presets/analyze/10x-vdj-bcr-full-length.yaml | 1 + regression/presets/analyze/10x-vdj-bcr.yaml | 1 + .../presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml | 1 + regression/presets/analyze/10x-vdj-tcr-full-length.yaml | 1 + regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml | 1 + regression/presets/analyze/10x-vdj-tcr-qc-test.yaml | 1 + regression/presets/analyze/10x-vdj-tcr.yaml | 1 + regression/presets/analyze/10x-vdj.yaml | 1 + regression/presets/analyze/abhelix-human-bcr-cdr3.yaml | 1 + regression/presets/analyze/abhelix-human-bcr-full-length.yaml | 1 + regression/presets/analyze/abhelix-human-tcr-cdr3.yaml | 1 + regression/presets/analyze/abhelix-human-tcr-full-length.yaml | 1 + regression/presets/analyze/abhelix-human.yaml | 1 + regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml | 1 + regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml | 1 + regression/presets/analyze/ampliseq-tcrb-plus.yaml | 1 + regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml | 1 + regression/presets/analyze/ampliseq-tcrb-sr.yaml | 1 + .../presets/analyze/bd-rhapsody-human-bcr-full-length.yaml | 1 + .../presets/analyze/bd-rhapsody-human-tcr-full-length.yaml | 1 + .../presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml | 1 + .../presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml | 1 + regression/presets/analyze/biomed2-human-bcr-cdr3.yaml | 1 + regression/presets/analyze/biomed2-human-bcr-full-length.yaml | 1 + regression/presets/analyze/biomed2-human-bcr.yaml | 1 + regression/presets/analyze/cellecta-air-human.yaml | 1 + regression/presets/analyze/exome-seq.yaml | 1 + regression/presets/analyze/flairr-seq.yaml | 1 + regression/presets/analyze/generic-amplicon-with-umi.yaml | 1 + regression/presets/analyze/generic-amplicon.yaml | 1 + regression/presets/analyze/generic-bcr-amplicon-umi.yaml | 1 + regression/presets/analyze/generic-bcr-amplicon.yaml | 1 + .../analyze/generic-ht-single-cell-amplicon-with-umi.yaml | 1 + regression/presets/analyze/generic-ht-single-cell-amplicon.yaml | 1 + .../analyze/generic-ht-single-cell-fragmented-with-umi.yaml | 1 + .../presets/analyze/generic-ht-single-cell-fragmented.yaml | 1 + .../analyze/generic-lt-single-cell-amplicon-with-umi.yaml | 1 + regression/presets/analyze/generic-lt-single-cell-amplicon.yaml | 1 + .../analyze/generic-lt-single-cell-fragmented-with-umi.yaml | 1 + .../presets/analyze/generic-lt-single-cell-fragmented.yaml | 1 + .../analyze/generic-tcr-amplicon-separate-samples-umi.yaml | 1 + regression/presets/analyze/generic-tcr-amplicon-umi.yaml | 1 + regression/presets/analyze/generic-tcr-amplicon.yaml | 1 + regression/presets/analyze/han-et-al-2014.yaml | 1 + regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml | 1 + regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml | 1 + regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml | 1 + regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml | 1 + regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml | 1 + regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml | 1 + regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml | 1 + regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml | 1 + regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml | 1 + regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml | 1 + regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml | 1 + regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml | 1 + regression/presets/analyze/irepertoire-repseq-human-dna-lr.yaml | 1 + regression/presets/analyze/irepertoire-repseq-human-dna-sr.yaml | 1 + regression/presets/analyze/irepertoire-repseq-human-lr.yaml | 1 + regression/presets/analyze/irepertoire-repseq-human-sr.yaml | 1 + regression/presets/analyze/irepertoire-repseq-mouse-lr.yaml | 1 + regression/presets/analyze/irepertoire-repseq-mouse-sr.yaml | 1 + regression/presets/analyze/irepertoire-repseq-plus-human.yaml | 1 + regression/presets/analyze/irepertoire-repseq-plus-mouse.yaml | 1 + regression/presets/analyze/mikelov-et-al-2021.yaml | 1 + regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml | 1 + .../presets/analyze/milab-human-bcr-multiplex-full-length.yaml | 1 + regression/presets/analyze/milab-human-ig-rna-multiplex.yaml | 1 + .../presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml | 1 + regression/presets/analyze/milab-human-tcr-dna-multiplex.yaml | 1 + .../presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml | 1 + regression/presets/analyze/milab-human-tcr-rna-multiplex.yaml | 1 + regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml | 1 + .../presets/analyze/milab-human-tcr-rna-race-full-length.yaml | 1 + regression/presets/analyze/milab-human-tcr-rna-race.yaml | 1 + regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml | 1 + .../presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml | 1 + regression/presets/analyze/milab-mouse-tcr-rna-race.yaml | 1 + regression/presets/analyze/nebnext-human-bcr-cdr3.yaml | 1 + regression/presets/analyze/nebnext-human-bcr-full-length.yaml | 1 + regression/presets/analyze/nebnext-human-immune-sequencing.yaml | 1 + regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml | 1 + .../presets/analyze/nebnext-human-tcr-bcr-full-length.yaml | 1 + regression/presets/analyze/nebnext-human-tcr-cdr3.yaml | 1 + regression/presets/analyze/nebnext-human-tcr-full-length.yaml | 1 + regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml | 1 + regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml | 1 + regression/presets/analyze/nebnext-mouse-immune-sequencing.yaml | 1 + regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml | 1 + .../presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml | 1 + regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml | 1 + regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml | 1 + regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml | 1 + .../presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml | 1 + .../presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml | 1 + regression/presets/analyze/oncomine-human-bcr-pan-clonality.yaml | 1 + regression/presets/analyze/oncomine-human-igh-fr1-j.yaml | 1 + regression/presets/analyze/oncomine-human-igh-fr2-j.yaml | 1 + regression/presets/analyze/oncomine-human-igh-fr3-j.yaml | 1 + regression/presets/analyze/oncomine-human-igh-leader-j.yaml | 1 + regression/presets/analyze/oncomine-human-igh-lr.yaml | 1 + regression/presets/analyze/oncomine-human-igh-sr.yaml | 1 + .../presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml | 1 + regression/presets/analyze/oncomine-human-tcr-pan-clonality.yaml | 1 + regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml | 1 + .../presets/analyze/oncomine-human-tcrb-lr-full-length.yaml | 1 + regression/presets/analyze/oncomine-human-tcrb-lr.yaml | 1 + regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml | 1 + regression/presets/analyze/oncomine-human-tcrb-sr.yaml | 1 + regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml | 1 + regression/presets/analyze/ont-rna-seq-vdj.yaml | 1 + regression/presets/analyze/parse-bio-3gex.yaml | 1 + regression/presets/analyze/parse-bio-vdj-3gex.yaml | 1 + regression/presets/analyze/pereshlop-test.yaml | 1 + regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml | 1 + regression/presets/analyze/qiaseq-human-tcr-full-length.yaml | 1 + regression/presets/analyze/qiaseq-human-tcr-panel.yaml | 1 + regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml | 1 + regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml | 1 + regression/presets/analyze/qiaseq-mouse-tcr-panel.yaml | 1 + regression/presets/analyze/rna-seq.yaml | 1 + regression/presets/analyze/seqwell-vdj-cdr3.yaml | 1 + regression/presets/analyze/seqwell-vdj.yaml | 1 + regression/presets/analyze/single-cell-as-sample-no-split.yaml | 1 + regression/presets/analyze/single-cell-as-sample-split.yaml | 1 + regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml | 1 + regression/presets/analyze/singleron-2.0.1-vdj.yaml | 1 + regression/presets/analyze/smartseq2-vdj-full-length.yaml | 1 + regression/presets/analyze/smartseq2-vdj.yaml | 1 + regression/presets/analyze/split-seq-3gex.yaml | 1 + regression/presets/analyze/split-seq-vdj-3gex.yaml | 1 + regression/presets/analyze/takara-human-bcr-cdr3.yaml | 1 + regression/presets/analyze/takara-human-bcr-full-length.yaml | 1 + regression/presets/analyze/takara-human-bcr-profiling.yaml | 1 + regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml | 1 + regression/presets/analyze/takara-human-tcr-V1-full-length.yaml | 1 + regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml | 1 + regression/presets/analyze/takara-human-tcr-V2-full-length.yaml | 1 + regression/presets/analyze/takara-human-tcr-profiling.yaml | 1 + regression/presets/analyze/takara-human-tcr-v2-profiling.yaml | 1 + regression/presets/analyze/takara-mouse-bcr-cdr3.yaml | 1 + regression/presets/analyze/takara-mouse-bcr-full-length.yaml | 1 + regression/presets/analyze/takara-mouse-bcr-profiling.yaml | 1 + regression/presets/analyze/takara-mouse-tcr-cdr3.yaml | 1 + regression/presets/analyze/takara-mouse-tcr-full-length.yaml | 1 + regression/presets/analyze/takara-mouse-tcr-profiling.yaml | 1 + regression/presets/analyze/takara-smartseq-human-bcr.yaml | 1 + regression/presets/analyze/takara-smartseq-human-tcr.yaml | 1 + regression/presets/analyze/test-airr-long-ig-base.yaml | 1 + regression/presets/analyze/test-generic.yaml | 1 + regression/presets/analyze/test-gf-intersection.yaml | 1 + .../presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml | 1 + .../presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml | 1 + regression/presets/analyze/test-subCloningRegions.yaml | 1 + regression/presets/analyze/test-tcr-shotgun.yaml | 1 + regression/presets/analyze/umi-guided-consensus-test.yaml | 1 + regression/presets/analyze/vergani-et-al-2017-cdr3.yaml | 1 + regression/presets/analyze/vergani-et-al-2017-full-length.yaml | 1 + 161 files changed, 161 insertions(+) diff --git a/regression/presets/analyze/10x-5gex-cdr3.yaml b/regression/presets/analyze/10x-5gex-cdr3.yaml index 0a36a5998..6b3603b32 100644 --- a/regression/presets/analyze/10x-5gex-cdr3.yaml +++ b/regression/presets/analyze/10x-5gex-cdr3.yaml @@ -390,6 +390,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-5gex-full-length.yaml b/regression/presets/analyze/10x-5gex-full-length.yaml index f76cad6df..a43195610 100644 --- a/regression/presets/analyze/10x-5gex-full-length.yaml +++ b/regression/presets/analyze/10x-5gex-full-length.yaml @@ -394,6 +394,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-5gex.yaml b/regression/presets/analyze/10x-5gex.yaml index 0a36a5998..6b3603b32 100644 --- a/regression/presets/analyze/10x-5gex.yaml +++ b/regression/presets/analyze/10x-5gex.yaml @@ -390,6 +390,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml index d28eccea4..a5ddf7960 100644 --- a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml @@ -500,6 +500,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml index 50d039391..a6d5ea991 100644 --- a/regression/presets/analyze/10x-vdj-bcr.yaml +++ b/regression/presets/analyze/10x-vdj-bcr.yaml @@ -496,6 +496,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore 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 index 676a1aefb..80c0f5b0b 100644 --- a/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml @@ -463,6 +463,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml index d28eccea4..a5ddf7960 100644 --- a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml @@ -500,6 +500,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml index c4b2bd976..f6dc7b8d5 100644 --- a/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml @@ -426,6 +426,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml index 2172b74b8..e6cf555bb 100644 --- a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml @@ -499,6 +499,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-vdj-tcr.yaml b/regression/presets/analyze/10x-vdj-tcr.yaml index 50d039391..a6d5ea991 100644 --- a/regression/presets/analyze/10x-vdj-tcr.yaml +++ b/regression/presets/analyze/10x-vdj-tcr.yaml @@ -496,6 +496,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/10x-vdj.yaml b/regression/presets/analyze/10x-vdj.yaml index 50d039391..a6d5ea991 100644 --- a/regression/presets/analyze/10x-vdj.yaml +++ b/regression/presets/analyze/10x-vdj.yaml @@ -496,6 +496,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml index 4245aed37..6b881ca11 100644 --- a/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/abhelix-human-bcr-full-length.yaml b/regression/presets/analyze/abhelix-human-bcr-full-length.yaml index 4e2a48631..241d3e928 100644 --- a/regression/presets/analyze/abhelix-human-bcr-full-length.yaml +++ b/regression/presets/analyze/abhelix-human-bcr-full-length.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml index 4245aed37..6b881ca11 100644 --- a/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/abhelix-human-tcr-full-length.yaml b/regression/presets/analyze/abhelix-human-tcr-full-length.yaml index 4e2a48631..241d3e928 100644 --- a/regression/presets/analyze/abhelix-human-tcr-full-length.yaml +++ b/regression/presets/analyze/abhelix-human-tcr-full-length.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/abhelix-human.yaml b/regression/presets/analyze/abhelix-human.yaml index 4e2a48631..241d3e928 100644 --- a/regression/presets/analyze/abhelix-human.yaml +++ b/regression/presets/analyze/abhelix-human.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml index c3be724cd..95d105717 100644 --- a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml index 4d93a9653..d56991766 100644 --- a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/ampliseq-tcrb-plus.yaml b/regression/presets/analyze/ampliseq-tcrb-plus.yaml index c3be724cd..95d105717 100644 --- a/regression/presets/analyze/ampliseq-tcrb-plus.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-plus.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml index 4d93a9653..d56991766 100644 --- a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/ampliseq-tcrb-sr.yaml b/regression/presets/analyze/ampliseq-tcrb-sr.yaml index 4d93a9653..d56991766 100644 --- a/regression/presets/analyze/ampliseq-tcrb-sr.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-sr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml index bef3ab248..2497e7b70 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml @@ -388,6 +388,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml index caac11e1d..a6737ab5c 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml @@ -367,6 +367,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml index e6cd793b2..e8c0cd065 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml @@ -388,6 +388,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml index 61a215468..238b19516 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml @@ -367,6 +367,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml b/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml index a86ae233c..c0f674b64 100644 --- a/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/biomed2-human-bcr-full-length.yaml b/regression/presets/analyze/biomed2-human-bcr-full-length.yaml index 98513f1bf..e9ce401f3 100644 --- a/regression/presets/analyze/biomed2-human-bcr-full-length.yaml +++ b/regression/presets/analyze/biomed2-human-bcr-full-length.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/biomed2-human-bcr.yaml b/regression/presets/analyze/biomed2-human-bcr.yaml index 98513f1bf..e9ce401f3 100644 --- a/regression/presets/analyze/biomed2-human-bcr.yaml +++ b/regression/presets/analyze/biomed2-human-bcr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/cellecta-air-human.yaml b/regression/presets/analyze/cellecta-air-human.yaml index c0651c779..2cf50f018 100644 --- a/regression/presets/analyze/cellecta-air-human.yaml +++ b/regression/presets/analyze/cellecta-air-human.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/exome-seq.yaml b/regression/presets/analyze/exome-seq.yaml index f7640bf25..2f237730d 100644 --- a/regression/presets/analyze/exome-seq.yaml +++ b/regression/presets/analyze/exome-seq.yaml @@ -234,6 +234,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/flairr-seq.yaml b/regression/presets/analyze/flairr-seq.yaml index 9505d771a..9bcd2b906 100644 --- a/regression/presets/analyze/flairr-seq.yaml +++ b/regression/presets/analyze/flairr-seq.yaml @@ -331,6 +331,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-amplicon-with-umi.yaml b/regression/presets/analyze/generic-amplicon-with-umi.yaml index fcec1b688..16345627a 100644 --- a/regression/presets/analyze/generic-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-amplicon-with-umi.yaml @@ -334,6 +334,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-amplicon.yaml b/regression/presets/analyze/generic-amplicon.yaml index 3226ea8b2..6f89fb5c1 100644 --- a/regression/presets/analyze/generic-amplicon.yaml +++ b/regression/presets/analyze/generic-amplicon.yaml @@ -271,6 +271,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-bcr-amplicon-umi.yaml b/regression/presets/analyze/generic-bcr-amplicon-umi.yaml index fcec1b688..16345627a 100644 --- a/regression/presets/analyze/generic-bcr-amplicon-umi.yaml +++ b/regression/presets/analyze/generic-bcr-amplicon-umi.yaml @@ -334,6 +334,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-bcr-amplicon.yaml b/regression/presets/analyze/generic-bcr-amplicon.yaml index 3226ea8b2..6f89fb5c1 100644 --- a/regression/presets/analyze/generic-bcr-amplicon.yaml +++ b/regression/presets/analyze/generic-bcr-amplicon.yaml @@ -271,6 +271,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml b/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml index 2f4949b3e..44d622dd9 100644 --- a/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml @@ -401,6 +401,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml b/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml index 3668ed488..7d80ee2e4 100644 --- a/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml @@ -349,6 +349,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml b/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml index c5f474ffb..d0d7d84f7 100644 --- a/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml @@ -403,6 +403,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml b/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml index c12da7286..568bf3974 100644 --- a/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml @@ -351,6 +351,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml b/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml index c142a9cae..36dfcb3ae 100644 --- a/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml @@ -369,6 +369,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml b/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml index c04fb495e..16c071b1f 100644 --- a/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml @@ -321,6 +321,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-lt-single-cell-fragmented-with-umi.yaml b/regression/presets/analyze/generic-lt-single-cell-fragmented-with-umi.yaml index a3ff9f1a7..dd71d339d 100644 --- a/regression/presets/analyze/generic-lt-single-cell-fragmented-with-umi.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-fragmented-with-umi.yaml @@ -371,6 +371,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml b/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml index d7dedc21a..099bfde2f 100644 --- a/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml @@ -323,6 +323,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml b/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml index 7be217856..0ddd2a888 100644 --- a/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml @@ -334,6 +334,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-tcr-amplicon-umi.yaml b/regression/presets/analyze/generic-tcr-amplicon-umi.yaml index fcec1b688..16345627a 100644 --- a/regression/presets/analyze/generic-tcr-amplicon-umi.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon-umi.yaml @@ -334,6 +334,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-tcr-amplicon.yaml b/regression/presets/analyze/generic-tcr-amplicon.yaml index 3226ea8b2..6f89fb5c1 100644 --- a/regression/presets/analyze/generic-tcr-amplicon.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon.yaml @@ -271,6 +271,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/han-et-al-2014.yaml b/regression/presets/analyze/han-et-al-2014.yaml index 51b2417d5..b4f2c94fd 100644 --- a/regression/presets/analyze/han-et-al-2014.yaml +++ b/regression/presets/analyze/han-et-al-2014.yaml @@ -346,6 +346,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml index 236310762..b5de4d190 100644 --- a/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml index 1ac693525..f56004e69 100644 --- a/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml index 236310762..b5de4d190 100644 --- a/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml index 1ac693525..f56004e69 100644 --- a/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml index 7a07da425..a88e1acbe 100644 --- a/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml index 4245aed37..6b881ca11 100644 --- a/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml index 7a07da425..a88e1acbe 100644 --- a/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml index 4245aed37..6b881ca11 100644 --- a/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml index ad42f4bbc..0756a783c 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml index 675779ebf..991a84780 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml index ad42f4bbc..0756a783c 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml index 675779ebf..991a84780 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-repseq-human-dna-lr.yaml b/regression/presets/analyze/irepertoire-repseq-human-dna-lr.yaml index 236310762..b5de4d190 100644 --- a/regression/presets/analyze/irepertoire-repseq-human-dna-lr.yaml +++ b/regression/presets/analyze/irepertoire-repseq-human-dna-lr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-repseq-human-dna-sr.yaml b/regression/presets/analyze/irepertoire-repseq-human-dna-sr.yaml index 1ac693525..f56004e69 100644 --- a/regression/presets/analyze/irepertoire-repseq-human-dna-sr.yaml +++ b/regression/presets/analyze/irepertoire-repseq-human-dna-sr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-repseq-human-lr.yaml b/regression/presets/analyze/irepertoire-repseq-human-lr.yaml index 7a07da425..a88e1acbe 100644 --- a/regression/presets/analyze/irepertoire-repseq-human-lr.yaml +++ b/regression/presets/analyze/irepertoire-repseq-human-lr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-repseq-human-sr.yaml b/regression/presets/analyze/irepertoire-repseq-human-sr.yaml index 4245aed37..6b881ca11 100644 --- a/regression/presets/analyze/irepertoire-repseq-human-sr.yaml +++ b/regression/presets/analyze/irepertoire-repseq-human-sr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-repseq-mouse-lr.yaml b/regression/presets/analyze/irepertoire-repseq-mouse-lr.yaml index ad42f4bbc..0756a783c 100644 --- a/regression/presets/analyze/irepertoire-repseq-mouse-lr.yaml +++ b/regression/presets/analyze/irepertoire-repseq-mouse-lr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-repseq-mouse-sr.yaml b/regression/presets/analyze/irepertoire-repseq-mouse-sr.yaml index 675779ebf..991a84780 100644 --- a/regression/presets/analyze/irepertoire-repseq-mouse-sr.yaml +++ b/regression/presets/analyze/irepertoire-repseq-mouse-sr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-repseq-plus-human.yaml b/regression/presets/analyze/irepertoire-repseq-plus-human.yaml index 7a07da425..a88e1acbe 100644 --- a/regression/presets/analyze/irepertoire-repseq-plus-human.yaml +++ b/regression/presets/analyze/irepertoire-repseq-plus-human.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/irepertoire-repseq-plus-mouse.yaml b/regression/presets/analyze/irepertoire-repseq-plus-mouse.yaml index ad42f4bbc..0756a783c 100644 --- a/regression/presets/analyze/irepertoire-repseq-plus-mouse.yaml +++ b/regression/presets/analyze/irepertoire-repseq-plus-mouse.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/mikelov-et-al-2021.yaml b/regression/presets/analyze/mikelov-et-al-2021.yaml index c9a763893..f158bfcf5 100644 --- a/regression/presets/analyze/mikelov-et-al-2021.yaml +++ b/regression/presets/analyze/mikelov-et-al-2021.yaml @@ -355,6 +355,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml index ebd0a6e0b..423aab780 100644 --- a/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml b/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml index 1f9a05068..f1790d17d 100644 --- a/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml +++ b/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-ig-rna-multiplex.yaml b/regression/presets/analyze/milab-human-ig-rna-multiplex.yaml index 1f9a05068..f1790d17d 100644 --- a/regression/presets/analyze/milab-human-ig-rna-multiplex.yaml +++ b/regression/presets/analyze/milab-human-ig-rna-multiplex.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml index 64e11b507..e3ef66fab 100644 --- a/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-tcr-dna-multiplex.yaml b/regression/presets/analyze/milab-human-tcr-dna-multiplex.yaml index 64e11b507..e3ef66fab 100644 --- a/regression/presets/analyze/milab-human-tcr-dna-multiplex.yaml +++ b/regression/presets/analyze/milab-human-tcr-dna-multiplex.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml index 2f01db175..eae4aa62a 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-tcr-rna-multiplex.yaml b/regression/presets/analyze/milab-human-tcr-rna-multiplex.yaml index 2f01db175..eae4aa62a 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-multiplex.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-multiplex.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml index 187ef847a..849aa685b 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml b/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml index cc7033de2..38cc49784 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-tcr-rna-race.yaml b/regression/presets/analyze/milab-human-tcr-rna-race.yaml index cc7033de2..38cc49784 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-race.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-race.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml b/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml index c070966cc..da16a9582 100644 --- a/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml +++ b/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml b/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml index 2706ad56e..8299ab137 100644 --- a/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml +++ b/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-mouse-tcr-rna-race.yaml b/regression/presets/analyze/milab-mouse-tcr-rna-race.yaml index 2706ad56e..8299ab137 100644 --- a/regression/presets/analyze/milab-mouse-tcr-rna-race.yaml +++ b/regression/presets/analyze/milab-mouse-tcr-rna-race.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml index 49d39eced..5c35861c1 100644 --- a/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-human-bcr-full-length.yaml b/regression/presets/analyze/nebnext-human-bcr-full-length.yaml index e5140294c..c4a4e8195 100644 --- a/regression/presets/analyze/nebnext-human-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-bcr-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-human-immune-sequencing.yaml b/regression/presets/analyze/nebnext-human-immune-sequencing.yaml index e5140294c..c4a4e8195 100644 --- a/regression/presets/analyze/nebnext-human-immune-sequencing.yaml +++ b/regression/presets/analyze/nebnext-human-immune-sequencing.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml index 49d39eced..5c35861c1 100644 --- a/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml b/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml index e5140294c..c4a4e8195 100644 --- a/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml index 49d39eced..5c35861c1 100644 --- a/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-human-tcr-full-length.yaml b/regression/presets/analyze/nebnext-human-tcr-full-length.yaml index e5140294c..c4a4e8195 100644 --- a/regression/presets/analyze/nebnext-human-tcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml index bc4bb8851..5fdd60ecc 100644 --- a/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml index c693b2374..78a6a4695 100644 --- a/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-mouse-immune-sequencing.yaml b/regression/presets/analyze/nebnext-mouse-immune-sequencing.yaml index c693b2374..78a6a4695 100644 --- a/regression/presets/analyze/nebnext-mouse-immune-sequencing.yaml +++ b/regression/presets/analyze/nebnext-mouse-immune-sequencing.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml index bc4bb8851..5fdd60ecc 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml index c693b2374..78a6a4695 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml index bc4bb8851..5fdd60ecc 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml index c693b2374..78a6a4695 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml index 4245aed37..6b881ca11 100644 --- a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml index 7a07da425..a88e1acbe 100644 --- a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml b/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml index 1ac693525..f56004e69 100644 --- a/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-bcr-pan-clonality.yaml b/regression/presets/analyze/oncomine-human-bcr-pan-clonality.yaml index 1ac693525..f56004e69 100644 --- a/regression/presets/analyze/oncomine-human-bcr-pan-clonality.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-pan-clonality.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml index 236310762..b5de4d190 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml index ae2c491e8..b8cb36778 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml index 1ac693525..f56004e69 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-igh-leader-j.yaml b/regression/presets/analyze/oncomine-human-igh-leader-j.yaml index 858065c69..e7257db17 100644 --- a/regression/presets/analyze/oncomine-human-igh-leader-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-leader-j.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-igh-lr.yaml b/regression/presets/analyze/oncomine-human-igh-lr.yaml index 7a07da425..a88e1acbe 100644 --- a/regression/presets/analyze/oncomine-human-igh-lr.yaml +++ b/regression/presets/analyze/oncomine-human-igh-lr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-igh-sr.yaml b/regression/presets/analyze/oncomine-human-igh-sr.yaml index 4d93a9653..d56991766 100644 --- a/regression/presets/analyze/oncomine-human-igh-sr.yaml +++ b/regression/presets/analyze/oncomine-human-igh-sr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml index 1ac693525..f56004e69 100644 --- a/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-tcr-pan-clonality.yaml b/regression/presets/analyze/oncomine-human-tcr-pan-clonality.yaml index 1ac693525..f56004e69 100644 --- a/regression/presets/analyze/oncomine-human-tcr-pan-clonality.yaml +++ b/regression/presets/analyze/oncomine-human-tcr-pan-clonality.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml index 4245aed37..6b881ca11 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml index 7a07da425..a88e1acbe 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr.yaml index 7a07da425..a88e1acbe 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-lr.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-lr.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml index 4d93a9653..d56991766 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/oncomine-human-tcrb-sr.yaml b/regression/presets/analyze/oncomine-human-tcrb-sr.yaml index 4d93a9653..d56991766 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-sr.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-sr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore 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 c501746c9..2c0ff6314 100644 --- a/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml +++ b/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml @@ -234,6 +234,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/ont-rna-seq-vdj.yaml b/regression/presets/analyze/ont-rna-seq-vdj.yaml index c501746c9..2c0ff6314 100644 --- a/regression/presets/analyze/ont-rna-seq-vdj.yaml +++ b/regression/presets/analyze/ont-rna-seq-vdj.yaml @@ -234,6 +234,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/parse-bio-3gex.yaml b/regression/presets/analyze/parse-bio-3gex.yaml index 0dfeeeaf7..68d44d61f 100644 --- a/regression/presets/analyze/parse-bio-3gex.yaml +++ b/regression/presets/analyze/parse-bio-3gex.yaml @@ -1211,6 +1211,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/parse-bio-vdj-3gex.yaml b/regression/presets/analyze/parse-bio-vdj-3gex.yaml index 0dfeeeaf7..68d44d61f 100644 --- a/regression/presets/analyze/parse-bio-vdj-3gex.yaml +++ b/regression/presets/analyze/parse-bio-vdj-3gex.yaml @@ -1211,6 +1211,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/pereshlop-test.yaml b/regression/presets/analyze/pereshlop-test.yaml index 805a18b6d..3ee5dd16c 100644 --- a/regression/presets/analyze/pereshlop-test.yaml +++ b/regression/presets/analyze/pereshlop-test.yaml @@ -261,6 +261,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml b/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml index 913363105..e123daa2c 100644 --- a/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml @@ -344,6 +344,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml b/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml index 04edb2843..6262f92fa 100644 --- a/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml +++ b/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml @@ -344,6 +344,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/qiaseq-human-tcr-panel.yaml b/regression/presets/analyze/qiaseq-human-tcr-panel.yaml index 04edb2843..6262f92fa 100644 --- a/regression/presets/analyze/qiaseq-human-tcr-panel.yaml +++ b/regression/presets/analyze/qiaseq-human-tcr-panel.yaml @@ -344,6 +344,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml index 4f956e32f..2be9af585 100644 --- a/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml @@ -344,6 +344,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml index d79be0f77..e08268123 100644 --- a/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml @@ -344,6 +344,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-panel.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-panel.yaml index d79be0f77..e08268123 100644 --- a/regression/presets/analyze/qiaseq-mouse-tcr-panel.yaml +++ b/regression/presets/analyze/qiaseq-mouse-tcr-panel.yaml @@ -344,6 +344,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/rna-seq.yaml b/regression/presets/analyze/rna-seq.yaml index 3befdcd5a..0f677de3b 100644 --- a/regression/presets/analyze/rna-seq.yaml +++ b/regression/presets/analyze/rna-seq.yaml @@ -261,6 +261,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/seqwell-vdj-cdr3.yaml b/regression/presets/analyze/seqwell-vdj-cdr3.yaml index 8b516bccc..f5944d974 100644 --- a/regression/presets/analyze/seqwell-vdj-cdr3.yaml +++ b/regression/presets/analyze/seqwell-vdj-cdr3.yaml @@ -398,6 +398,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/seqwell-vdj.yaml b/regression/presets/analyze/seqwell-vdj.yaml index 8b516bccc..f5944d974 100644 --- a/regression/presets/analyze/seqwell-vdj.yaml +++ b/regression/presets/analyze/seqwell-vdj.yaml @@ -398,6 +398,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/single-cell-as-sample-no-split.yaml b/regression/presets/analyze/single-cell-as-sample-no-split.yaml index 8c41deaf6..59d7d2cb9 100644 --- a/regression/presets/analyze/single-cell-as-sample-no-split.yaml +++ b/regression/presets/analyze/single-cell-as-sample-no-split.yaml @@ -342,6 +342,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/single-cell-as-sample-split.yaml b/regression/presets/analyze/single-cell-as-sample-split.yaml index 6fe58612b..e153f98db 100644 --- a/regression/presets/analyze/single-cell-as-sample-split.yaml +++ b/regression/presets/analyze/single-cell-as-sample-split.yaml @@ -334,6 +334,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml b/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml index c054c71f1..6c00af973 100644 --- a/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml +++ b/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml @@ -369,6 +369,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/singleron-2.0.1-vdj.yaml b/regression/presets/analyze/singleron-2.0.1-vdj.yaml index c054c71f1..6c00af973 100644 --- a/regression/presets/analyze/singleron-2.0.1-vdj.yaml +++ b/regression/presets/analyze/singleron-2.0.1-vdj.yaml @@ -369,6 +369,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/smartseq2-vdj-full-length.yaml b/regression/presets/analyze/smartseq2-vdj-full-length.yaml index 040b53d31..f3bc013de 100644 --- a/regression/presets/analyze/smartseq2-vdj-full-length.yaml +++ b/regression/presets/analyze/smartseq2-vdj-full-length.yaml @@ -323,6 +323,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/smartseq2-vdj.yaml b/regression/presets/analyze/smartseq2-vdj.yaml index 040b53d31..f3bc013de 100644 --- a/regression/presets/analyze/smartseq2-vdj.yaml +++ b/regression/presets/analyze/smartseq2-vdj.yaml @@ -323,6 +323,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/split-seq-3gex.yaml b/regression/presets/analyze/split-seq-3gex.yaml index 07ad6baa9..03622464b 100644 --- a/regression/presets/analyze/split-seq-3gex.yaml +++ b/regression/presets/analyze/split-seq-3gex.yaml @@ -1017,6 +1017,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/split-seq-vdj-3gex.yaml b/regression/presets/analyze/split-seq-vdj-3gex.yaml index 07ad6baa9..03622464b 100644 --- a/regression/presets/analyze/split-seq-vdj-3gex.yaml +++ b/regression/presets/analyze/split-seq-vdj-3gex.yaml @@ -1017,6 +1017,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-bcr-cdr3.yaml b/regression/presets/analyze/takara-human-bcr-cdr3.yaml index 3c60e104a..e0ec49c65 100644 --- a/regression/presets/analyze/takara-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/takara-human-bcr-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-bcr-full-length.yaml b/regression/presets/analyze/takara-human-bcr-full-length.yaml index 9a700885a..c3f0afefd 100644 --- a/regression/presets/analyze/takara-human-bcr-full-length.yaml +++ b/regression/presets/analyze/takara-human-bcr-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-bcr-profiling.yaml b/regression/presets/analyze/takara-human-bcr-profiling.yaml index 9a700885a..c3f0afefd 100644 --- a/regression/presets/analyze/takara-human-bcr-profiling.yaml +++ b/regression/presets/analyze/takara-human-bcr-profiling.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml b/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml index ed446b146..d736f28f7 100644 --- a/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml +++ b/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml b/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml index da4c239a5..24b5d64c0 100644 --- a/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml +++ b/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml b/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml index 0dd366b7a..218a2c8d5 100644 --- a/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml +++ b/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml b/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml index df827dcca..0fa732b43 100644 --- a/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml +++ b/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-tcr-profiling.yaml b/regression/presets/analyze/takara-human-tcr-profiling.yaml index da4c239a5..24b5d64c0 100644 --- a/regression/presets/analyze/takara-human-tcr-profiling.yaml +++ b/regression/presets/analyze/takara-human-tcr-profiling.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-human-tcr-v2-profiling.yaml b/regression/presets/analyze/takara-human-tcr-v2-profiling.yaml index df827dcca..0fa732b43 100644 --- a/regression/presets/analyze/takara-human-tcr-v2-profiling.yaml +++ b/regression/presets/analyze/takara-human-tcr-v2-profiling.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml b/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml index 5716348ef..611653f67 100644 --- a/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml +++ b/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-mouse-bcr-full-length.yaml b/regression/presets/analyze/takara-mouse-bcr-full-length.yaml index 1a2d6da6a..31115a75d 100644 --- a/regression/presets/analyze/takara-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/takara-mouse-bcr-full-length.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-mouse-bcr-profiling.yaml b/regression/presets/analyze/takara-mouse-bcr-profiling.yaml index 1a2d6da6a..31115a75d 100644 --- a/regression/presets/analyze/takara-mouse-bcr-profiling.yaml +++ b/regression/presets/analyze/takara-mouse-bcr-profiling.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml b/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml index 5716348ef..611653f67 100644 --- a/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-mouse-tcr-full-length.yaml b/regression/presets/analyze/takara-mouse-tcr-full-length.yaml index 1a2d6da6a..31115a75d 100644 --- a/regression/presets/analyze/takara-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/takara-mouse-tcr-full-length.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-mouse-tcr-profiling.yaml b/regression/presets/analyze/takara-mouse-tcr-profiling.yaml index 1a2d6da6a..31115a75d 100644 --- a/regression/presets/analyze/takara-mouse-tcr-profiling.yaml +++ b/regression/presets/analyze/takara-mouse-tcr-profiling.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-smartseq-human-bcr.yaml b/regression/presets/analyze/takara-smartseq-human-bcr.yaml index 9a700885a..c3f0afefd 100644 --- a/regression/presets/analyze/takara-smartseq-human-bcr.yaml +++ b/regression/presets/analyze/takara-smartseq-human-bcr.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/takara-smartseq-human-tcr.yaml b/regression/presets/analyze/takara-smartseq-human-tcr.yaml index df827dcca..0fa732b43 100644 --- a/regression/presets/analyze/takara-smartseq-human-tcr.yaml +++ b/regression/presets/analyze/takara-smartseq-human-tcr.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/test-airr-long-ig-base.yaml b/regression/presets/analyze/test-airr-long-ig-base.yaml index a58e45fd0..3bc0a058f 100644 --- a/regression/presets/analyze/test-airr-long-ig-base.yaml +++ b/regression/presets/analyze/test-airr-long-ig-base.yaml @@ -267,6 +267,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/test-generic.yaml b/regression/presets/analyze/test-generic.yaml index bb1ae5c3c..6f584dc92 100644 --- a/regression/presets/analyze/test-generic.yaml +++ b/regression/presets/analyze/test-generic.yaml @@ -269,6 +269,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/test-gf-intersection.yaml b/regression/presets/analyze/test-gf-intersection.yaml index 4d3229807..338e82ba6 100644 --- a/regression/presets/analyze/test-gf-intersection.yaml +++ b/regression/presets/analyze/test-gf-intersection.yaml @@ -330,6 +330,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml b/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml index 86654e90f..e2d914700 100644 --- a/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml +++ b/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml @@ -356,6 +356,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml b/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml index c9a763893..f158bfcf5 100644 --- a/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml +++ b/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml @@ -355,6 +355,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/test-subCloningRegions.yaml b/regression/presets/analyze/test-subCloningRegions.yaml index 71190ee53..3847c0c87 100644 --- a/regression/presets/analyze/test-subCloningRegions.yaml +++ b/regression/presets/analyze/test-subCloningRegions.yaml @@ -272,6 +272,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/test-tcr-shotgun.yaml b/regression/presets/analyze/test-tcr-shotgun.yaml index 0ecbbaf22..ac6203028 100644 --- a/regression/presets/analyze/test-tcr-shotgun.yaml +++ b/regression/presets/analyze/test-tcr-shotgun.yaml @@ -260,6 +260,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/umi-guided-consensus-test.yaml b/regression/presets/analyze/umi-guided-consensus-test.yaml index d74356b28..4c3519157 100644 --- a/regression/presets/analyze/umi-guided-consensus-test.yaml +++ b/regression/presets/analyze/umi-guided-consensus-test.yaml @@ -312,6 +312,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml b/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml index 16adda550..f5eddef83 100644 --- a/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml +++ b/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/vergani-et-al-2017-full-length.yaml b/regression/presets/analyze/vergani-et-al-2017-full-length.yaml index 3c2d58502..2c8d12deb 100644 --- a/regression/presets/analyze/vergani-et-al-2017-full-length.yaml +++ b/regression/presets/analyze/vergani-et-al-2017-full-length.yaml @@ -329,6 +329,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore From f1a715d19cb7f70fe7540684c2b733052cc70c9b Mon Sep 17 00:00:00 2001 From: gnefedev Date: Tue, 27 Jun 2023 09:38:13 +0200 Subject: [PATCH 06/15] fix test --- .../com/milaboratory/mixcr/PresetsTest.kt | 76 ++++++++++--------- 1 file changed, 39 insertions(+), 37 deletions(-) diff --git a/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt b/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt index 6bc3cdca1..91362ddb2 100644 --- a/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt +++ b/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt @@ -10,12 +10,14 @@ import com.milaboratory.mixcr.basictypes.tag.TagsInfo import com.milaboratory.mixcr.cli.presetFlagsMessages import com.milaboratory.mixcr.export.CloneFieldsExtractorsFactory import com.milaboratory.mixcr.export.MetaForExport +import com.milaboratory.mixcr.export.VDJCAlignmentsFieldsExtractorsFactory import com.milaboratory.mixcr.presets.MiXCRParamsBundle import com.milaboratory.mixcr.presets.MiXCRStepReports import com.milaboratory.mixcr.presets.Presets import com.milaboratory.test.TestUtil.assertJson import com.milaboratory.util.K_OM import com.milaboratory.util.K_YAML_OM +import io.kotest.assertions.asClue import io.kotest.assertions.throwables.shouldNotThrowAny import io.kotest.assertions.withClue import org.junit.Assert @@ -86,43 +88,43 @@ class PresetsTest { @Test fun testExport2() { for (presetName in Presets.nonAbstractPresetNames) { - val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName) - if (bundle.align == null) - continue - val tagsInfo = TagsInfo( - 0, - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL", 0), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL1", 1), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL1ROW", 2), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL2", 3), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL2COLUMN", 4), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL3", 5), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL3PLATE", 6), - TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI", 7), - TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI1", 8), - TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI2", 9), - TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI3", 10), - ) - val metaForExport = MetaForExport( - listOf(tagsInfo), - null, - MiXCRStepReports() - ) - bundle.exportAlignments?.let { al -> - println( - CloneFieldsExtractorsFactory.createExtractors( - al.fields, - metaForExport - ).size - ) - } - bundle.exportClones?.let { al -> - println( - CloneFieldsExtractorsFactory.createExtractors( - al.fields, // .filter { !it.field.contains("tag", ignoreCase = true) } - metaForExport - ).size - ) + presetName.asClue { + shouldNotThrowAny { + val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName) + if (bundle.align != null) { + val tagsInfo = TagsInfo( + 0, + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL", 0), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL1", 1), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL1ROW", 2), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL2", 3), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL2COLUMN", 4), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL3", 5), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL3PLATE", 6), + TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI", 7), + TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI1", 8), + TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI2", 9), + TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI3", 10), + ) + val metaForExport = MetaForExport( + listOf(tagsInfo), + null, + MiXCRStepReports() + ) + bundle.exportAlignments?.let { al -> + VDJCAlignmentsFieldsExtractorsFactory.createExtractors( + al.fields, + metaForExport + ).size + } + bundle.exportClones?.let { al -> + CloneFieldsExtractorsFactory.createExtractors( + al.fields, // .filter { !it.field.contains("tag", ignoreCase = true) } + metaForExport + ).size + } + } + } } } } From 13583f17eb28b7e4a1086a92cc1fd327ad7d1efe Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 29 Jun 2023 14:55:26 +0200 Subject: [PATCH 07/15] write empty file on exportClones if there is no clones --- .../cli/CommandExportAlignmentsPretty.kt | 6 ++---- .../mixcr/cli/CommandExportClones.kt | 19 +++++++++++-------- 2 files changed, 13 insertions(+), 12 deletions(-) diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt index 2c2d78c1c..833f86843 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportAlignmentsPretty.kt @@ -34,11 +34,10 @@ import picocli.CommandLine.Command import picocli.CommandLine.Help.Visibility.ALWAYS import picocli.CommandLine.Option import picocli.CommandLine.Parameters -import java.io.BufferedOutputStream -import java.io.FileOutputStream import java.io.PrintStream import java.nio.file.Path import java.util.* +import kotlin.io.path.outputStream @Command( description = ["Export verbose information about alignments."] @@ -225,8 +224,7 @@ class CommandExportAlignmentsPretty : MiXCRCommandWithOutputs() { CommandExportAlignments.openAlignmentsPort(input).use { readerAndHeader -> ValidationException.chainsExist(chains, readerAndHeader.usedGenes) - (out?.let { PrintStream(BufferedOutputStream(FileOutputStream(it.toFile()), 32768)) } - ?: System.out).use { output -> + (out?.let { PrintStream(it.outputStream().buffered(32768)) } ?: System.out).use { output -> readerAndHeader.port.use { reader -> val countBefore = limitBefore ?: Int.MAX_VALUE val countAfter = limitAfter ?: Int.MAX_VALUE diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt index 1a334ae3e..0d3705a05 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportClones.kt @@ -226,16 +226,10 @@ object CommandExportClones { // Calculating splitting keys val splitFileKeys = params.splitFilesBy val splitFileKeyExtractors: List = splitFileKeys.map { - parseGroupingKey( - fileInfo.header, - it - ) + parseGroupingKey(fileInfo.header, it) } val groupByKeyExtractors: List = params.groupClonesBy.map { - parseGroupingKey( - fileInfo.header, - it - ) + parseGroupingKey(fileInfo.header, it) } val headerForExport = MetaForExport(fileInfo) @@ -330,6 +324,15 @@ object CommandExportClones { System.err.println("Exporting $keyString") runExport(set, Path(sFileName.render(fileNameSV))) } + + // in case of empty set, can't split, so can't calculate file names. + if (initialSet.size() == 0) { + // write empty file with headers (if headers are requested) + val writer = InfoWriter.create(outputFile, fieldExtractors, !params.noHeader) { + RowMetaForExport(initialSet.tagsInfo, headerForExport, exportDefaults.notCoveredAsEmpty) + } + writer.close() + } } } From 6f7c2a3bb311a0a76d52864ff1d0271b267b8683 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 29 Jun 2023 16:18:03 +0200 Subject: [PATCH 08/15] validation exception on request of feature that can't be translated --- changelogs/v4.4.md | 1 + .../mixcr/cli/CommandExportShmTreesAbstract.kt | 7 +++++-- .../milaboratory/mixcr/cli/CommandExportShmTreesPlots.kt | 9 ++++++--- 3 files changed, 12 insertions(+), 5 deletions(-) diff --git a/changelogs/v4.4.md b/changelogs/v4.4.md index d68ca2517..b57a16201 100644 --- a/changelogs/v4.4.md +++ b/changelogs/v4.4.md @@ -153,6 +153,7 @@ - remove de novo alleles that are actually the same, will be left only one - `findAlleles` will remove not used genes from library (genes that not represented in given donor) - make `--chains` optional in `downsampling` command and allow multiple input +- write empty file on `exportClones` if file doesn't contain any clones ## Braking changes diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesAbstract.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesAbstract.kt index c8aef4c9f..342d8a7e7 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesAbstract.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesAbstract.kt @@ -13,6 +13,7 @@ package com.milaboratory.mixcr.cli import com.milaboratory.app.InputFileType import com.milaboratory.app.ValidationException +import com.milaboratory.mixcr.export.GeneFeaturesExportUtil.checkAAComparable import com.milaboratory.mixcr.postanalysis.plots.SeqPattern import com.milaboratory.mixcr.trees.SHMTreesWriter.Companion.shmFileExtension import com.milaboratory.mixcr.trees.TreeFilter @@ -134,10 +135,12 @@ abstract class CommandExportShmTreesAbstract : MiXCRCommandWithOutputs() { private val pattern by lazy { patternOptions?.let { options -> - if (options.pattern.seqNt != null) + if (options.pattern.seqNt != null) { SeqPattern(options.pattern.seqNt!!, false, options.inFeature, options.maxErrors) - else + } else { + checkAAComparable(options.inFeature) SeqPattern(options.pattern.seqAa!!, true, options.inFeature, options.maxErrors) + } } } diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesPlots.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesPlots.kt index 9cdd120d6..0884a75f3 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesPlots.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandExportShmTreesPlots.kt @@ -15,6 +15,7 @@ import com.milaboratory.app.InputFileType import com.milaboratory.app.ValidationException import com.milaboratory.miplots.writePDF import com.milaboratory.mixcr.cli.CommonDescriptions.Labels +import com.milaboratory.mixcr.export.GeneFeaturesExportUtil.checkAAComparable import com.milaboratory.mixcr.postanalysis.plots.AlignmentOption import com.milaboratory.mixcr.postanalysis.plots.DefaultMeta import com.milaboratory.mixcr.postanalysis.plots.ShmTreePlotter @@ -135,12 +136,14 @@ class CommandExportShmTreesPlots : CommandExportShmTreesAbstract() { } val alignment by lazy { - if (alignmentGeneFeatureAa == null && alignmentGeneFeatureNt == null) + if (alignmentGeneFeatureAa == null && alignmentGeneFeatureNt == null) { null - else if (alignmentGeneFeatureAa != null) + } else if (alignmentGeneFeatureAa != null) { + checkAAComparable(alignmentGeneFeatureAa!!) AlignmentOption(alignmentGeneFeatureAa!!, true, !noAlignmentFill) - else + } else { AlignmentOption(alignmentGeneFeatureNt!!, false, !noAlignmentFill) + } } override fun run1() { From 1c89f47920149479b69397f75725087fc90de1e1 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 29 Jun 2023 17:38:30 +0200 Subject: [PATCH 09/15] better validation of args on export --- changelogs/v4.4.md | 1 + src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.kt | 3 ++- .../com/milaboratory/mixcr/export/FieldExtractorsTest.kt | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/changelogs/v4.4.md b/changelogs/v4.4.md index b57a16201..8c1bb1e08 100644 --- a/changelogs/v4.4.md +++ b/changelogs/v4.4.md @@ -154,6 +154,7 @@ - `findAlleles` will remove not used genes from library (genes that not represented in given donor) - make `--chains` optional in `downsampling` command and allow multiple input - write empty file on `exportClones` if file doesn't contain any clones +- better exception messages on incorrect inputs for export commands ## Braking changes diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.kt index 9714a44f9..e38e762ec 100644 --- a/src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.kt +++ b/src/main/kotlin/com/milaboratory/mixcr/cli/ExportUtil.kt @@ -45,10 +45,11 @@ fun FieldExtractorsFactory.addOptionsToSpec( if (argsCountToAdd > args.size) { throw ValidationException("Not enough parameters for ${field.cmdArgName}") } - val actualArgs: MutableList = mutableListOf() + val actualArgs = mutableListOf() repeat(argsCountToAdd) { actualArgs.add(args.pop()) } + field.tryParseArgs(actualArgs) fieldsCollector += ExportFieldDescription(field.cmdArgName, actualArgs) } .arity(field.arity.toString()) diff --git a/src/test/kotlin/com/milaboratory/mixcr/export/FieldExtractorsTest.kt b/src/test/kotlin/com/milaboratory/mixcr/export/FieldExtractorsTest.kt index 14ccca85b..e288909ac 100644 --- a/src/test/kotlin/com/milaboratory/mixcr/export/FieldExtractorsTest.kt +++ b/src/test/kotlin/com/milaboratory/mixcr/export/FieldExtractorsTest.kt @@ -48,7 +48,7 @@ class FieldExtractorsTest { val extractor = VDJCAlignmentsFieldsExtractorsFactory.fields .filter { it.cmdArgName == "-defaultAnchorPoints" } .flatMap { - it.createFields(MetaForExport(emptyList(), null, MiXCRStepReports()), emptyArray()) + it.createFields(MetaForExport(emptyList(), null, MiXCRStepReports()), emptyList()) } .first() val goAssert: F6 = object : F6 { From 6a9f2b9c090ff438eb9a299854e7759694fbf6b3 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Thu, 29 Jun 2023 21:52:36 +0200 Subject: [PATCH 10/15] update version --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 586804be0..0fe604285 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -130,7 +130,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.3.0-208-develop" +val mixcrAlgoVersion = "4.3.0-212-tiny-things" val milibVersion = "" val mitoolVersion = "" val repseqioVersion = "" From 0cb5643e2d4eed7b53c40e75a3113794aa4e4f65 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Fri, 30 Jun 2023 07:57:40 +0200 Subject: [PATCH 11/15] update version --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 0fe604285..1d13c0020 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -130,7 +130,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.3.0-212-tiny-things" +val mixcrAlgoVersion = "4.3.0-214-tiny-things" val milibVersion = "" val mitoolVersion = "" val repseqioVersion = "" From b329471ece87412364e88bbeb10d7e92988687f9 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Fri, 30 Jun 2023 06:13:39 +0000 Subject: [PATCH 12/15] regression tests automated change --- regression/presets/analyze/biomed2-human-igh.yaml | 1 + regression/presets/analyze/biomed2-human-igl-igk.yaml | 1 + regression/presets/analyze/biomed2-human-tcr.yaml | 1 + regression/presets/analyze/generic-single-cell-gex-with-umi.yaml | 1 + regression/presets/analyze/generic-single-cell-gex.yaml | 1 + regression/presets/analyze/milab-human-7genes-dna-multiplex.yaml | 1 + regression/presets/analyze/parse-bio-3gex-wt-mega.yaml | 1 + regression/presets/analyze/parse-bio-3gex-wt-mini.yaml | 1 + regression/presets/analyze/parse-bio-3gex-wt.yaml | 1 + .../presets/analyze/singleron-gexscope-single-cell-vdj.yaml | 1 + 10 files changed, 10 insertions(+) diff --git a/regression/presets/analyze/biomed2-human-igh.yaml b/regression/presets/analyze/biomed2-human-igh.yaml index 91e17fdc8..ba1c4e8c5 100644 --- a/regression/presets/analyze/biomed2-human-igh.yaml +++ b/regression/presets/analyze/biomed2-human-igh.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/biomed2-human-igl-igk.yaml b/regression/presets/analyze/biomed2-human-igl-igk.yaml index 8469c9965..deb370d4e 100644 --- a/regression/presets/analyze/biomed2-human-igl-igk.yaml +++ b/regression/presets/analyze/biomed2-human-igl-igk.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/biomed2-human-tcr.yaml b/regression/presets/analyze/biomed2-human-tcr.yaml index 8469c9965..deb370d4e 100644 --- a/regression/presets/analyze/biomed2-human-tcr.yaml +++ b/regression/presets/analyze/biomed2-human-tcr.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml b/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml index 1327fd14a..da04433f9 100644 --- a/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml +++ b/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml @@ -328,6 +328,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/generic-single-cell-gex.yaml b/regression/presets/analyze/generic-single-cell-gex.yaml index b3abff2f4..2f6b7766c 100644 --- a/regression/presets/analyze/generic-single-cell-gex.yaml +++ b/regression/presets/analyze/generic-single-cell-gex.yaml @@ -323,6 +323,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/milab-human-7genes-dna-multiplex.yaml b/regression/presets/analyze/milab-human-7genes-dna-multiplex.yaml index 6415592fa..fb6cc0888 100644 --- a/regression/presets/analyze/milab-human-7genes-dna-multiplex.yaml +++ b/regression/presets/analyze/milab-human-7genes-dna-multiplex.yaml @@ -240,6 +240,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/parse-bio-3gex-wt-mega.yaml b/regression/presets/analyze/parse-bio-3gex-wt-mega.yaml index 2d2225b1d..e8609ddaf 100644 --- a/regression/presets/analyze/parse-bio-3gex-wt-mega.yaml +++ b/regression/presets/analyze/parse-bio-3gex-wt-mega.yaml @@ -1136,6 +1136,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/parse-bio-3gex-wt-mini.yaml b/regression/presets/analyze/parse-bio-3gex-wt-mini.yaml index 8f0bb2843..ef9808d33 100644 --- a/regression/presets/analyze/parse-bio-3gex-wt-mini.yaml +++ b/regression/presets/analyze/parse-bio-3gex-wt-mini.yaml @@ -800,6 +800,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/parse-bio-3gex-wt.yaml b/regression/presets/analyze/parse-bio-3gex-wt.yaml index c8f121e01..ae610b27c 100644 --- a/regression/presets/analyze/parse-bio-3gex-wt.yaml +++ b/regression/presets/analyze/parse-bio-3gex-wt.yaml @@ -944,6 +944,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore diff --git a/regression/presets/analyze/singleron-gexscope-single-cell-vdj.yaml b/regression/presets/analyze/singleron-gexscope-single-cell-vdj.yaml index 927168ab4..a4b708a19 100644 --- a/regression/presets/analyze/singleron-gexscope-single-cell-vdj.yaml +++ b/regression/presets/analyze/singleron-gexscope-single-cell-vdj.yaml @@ -369,6 +369,7 @@ exportAlignments: chains: ALL noHeader: false fields: + - field: -readIds - field: -targetSequences - field: -targetQualities - field: -vHitsWithScore From 853e2d0cbeb085e5e73a86a2357b68bf4b5ba762 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Fri, 30 Jun 2023 09:28:54 +0200 Subject: [PATCH 13/15] `no_d_gene` in exportClones --- build.gradle.kts | 2 +- changelogs/v4.4.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 1d13c0020..dc56fbe21 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -130,7 +130,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.3.0-214-tiny-things" +val mixcrAlgoVersion = "4.3.0-215-tiny-things" val milibVersion = "" val mitoolVersion = "" val repseqioVersion = "" diff --git a/changelogs/v4.4.md b/changelogs/v4.4.md index 8c1bb1e08..08ab8d750 100644 --- a/changelogs/v4.4.md +++ b/changelogs/v4.4.md @@ -155,6 +155,7 @@ - make `--chains` optional in `downsampling` command and allow multiple input - write empty file on `exportClones` if file doesn't contain any clones - better exception messages on incorrect inputs for export commands +- on `exportClones` write `no_d_gene` if requested VDJunction, DCDR3Part or DJJunction in absence of D hit ## Braking changes From c2071bd8f6e6a76990b98a648a5bb4f918e8cfb2 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Fri, 30 Jun 2023 09:45:37 +0200 Subject: [PATCH 14/15] tests for presets contain --- src/main/resources/presets/protocols/bd.yaml | 4 +- .../com/milaboratory/mixcr/PresetsTest.kt | 82 +++++++++++-------- 2 files changed, 53 insertions(+), 33 deletions(-) diff --git a/src/main/resources/presets/protocols/bd.yaml b/src/main/resources/presets/protocols/bd.yaml index 7c1f68629..b33762917 100644 --- a/src/main/resources/presets/protocols/bd.yaml +++ b/src/main/resources/presets/protocols/bd.yaml @@ -7,6 +7,8 @@ - exportClones align: inheritFrom: align-single-cell + exportAlignments: + inheritFrom: exportAlignments-base refineTagsAndSort: whitelists: CELL1: builtin:rhapsody-cell1 @@ -539,4 +541,4 @@ inheritFrom: bd-rhapsody-tcr-full-length-base mixins: - type: SetSpecies - species: hsa \ No newline at end of file + species: hsa diff --git a/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt b/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt index 91362ddb2..757ed4edc 100644 --- a/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt +++ b/src/test/kotlin/com/milaboratory/mixcr/PresetsTest.kt @@ -11,6 +11,7 @@ import com.milaboratory.mixcr.cli.presetFlagsMessages import com.milaboratory.mixcr.export.CloneFieldsExtractorsFactory import com.milaboratory.mixcr.export.MetaForExport import com.milaboratory.mixcr.export.VDJCAlignmentsFieldsExtractorsFactory +import com.milaboratory.mixcr.presets.MiXCRCommandDescriptor import com.milaboratory.mixcr.presets.MiXCRParamsBundle import com.milaboratory.mixcr.presets.MiXCRStepReports import com.milaboratory.mixcr.presets.Presets @@ -20,6 +21,7 @@ import com.milaboratory.util.K_YAML_OM import io.kotest.assertions.asClue import io.kotest.assertions.throwables.shouldNotThrowAny import io.kotest.assertions.withClue +import io.kotest.matchers.shouldBe import org.junit.Assert import org.junit.Test import java.nio.file.Paths @@ -91,38 +93,36 @@ class PresetsTest { presetName.asClue { shouldNotThrowAny { val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName) - if (bundle.align != null) { - val tagsInfo = TagsInfo( - 0, - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL", 0), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL1", 1), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL1ROW", 2), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL2", 3), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL2COLUMN", 4), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL3", 5), - TagInfo(TagType.Cell, TagValueType.Sequence, "CELL3PLATE", 6), - TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI", 7), - TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI1", 8), - TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI2", 9), - TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI3", 10), - ) - val metaForExport = MetaForExport( - listOf(tagsInfo), - null, - MiXCRStepReports() - ) - bundle.exportAlignments?.let { al -> - VDJCAlignmentsFieldsExtractorsFactory.createExtractors( - al.fields, - metaForExport - ).size - } - bundle.exportClones?.let { al -> - CloneFieldsExtractorsFactory.createExtractors( - al.fields, // .filter { !it.field.contains("tag", ignoreCase = true) } - metaForExport - ).size - } + val tagsInfo = TagsInfo( + 0, + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL", 0), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL1", 1), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL1ROW", 2), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL2", 3), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL2COLUMN", 4), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL3", 5), + TagInfo(TagType.Cell, TagValueType.Sequence, "CELL3PLATE", 6), + TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI", 7), + TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI1", 8), + TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI2", 9), + TagInfo(TagType.Molecule, TagValueType.Sequence, "UMI3", 10), + ) + val metaForExport = MetaForExport( + listOf(tagsInfo), + null, + MiXCRStepReports() + ) + bundle.exportAlignments?.let { al -> + VDJCAlignmentsFieldsExtractorsFactory.createExtractors( + al.fields, + metaForExport + ).size + } + bundle.exportClones?.let { al -> + CloneFieldsExtractorsFactory.createExtractors( + al.fields, // .filter { !it.field.contains("tag", ignoreCase = true) } + metaForExport + ).size } } } @@ -142,4 +142,22 @@ class PresetsTest { } } } + + @Test + fun `all presets should have exportClones step`() { + Presets.nonAbstractPresetNames.filter { presetName -> + val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName) + MiXCRCommandDescriptor.exportClones !in bundle.pipeline!!.steps + } shouldBe emptyList() + } + + @Test + fun `all presets should have settings for exportAlignments`() { + Presets.nonAbstractPresetNames + .filter { !it.contains("-legacy-v") } + .filter { presetName -> + val bundle = Presets.MiXCRBundleResolver.resolvePreset(presetName) + bundle.exportAlignments == null + } shouldBe emptyList() + } } From d81b088aaf61770108ff6c60a3fe32fb409b1d04 Mon Sep 17 00:00:00 2001 From: gnefedev Date: Fri, 30 Jun 2023 07:58:49 +0000 Subject: [PATCH 15/15] regression tests automated change --- .../analyze/bd-rhapsody-human-bcr-v1.yaml | 19 ++++++++++++++++++- .../analyze/bd-rhapsody-human-bcr-v2.yaml | 19 ++++++++++++++++++- .../analyze/bd-rhapsody-human-tcr-v1.yaml | 19 ++++++++++++++++++- .../analyze/bd-rhapsody-human-tcr-v2.yaml | 19 ++++++++++++++++++- .../analyze/bd-rhapsody-mouse-bcr-v1.yaml | 19 ++++++++++++++++++- .../analyze/bd-rhapsody-mouse-bcr-v2.yaml | 19 ++++++++++++++++++- .../analyze/bd-rhapsody-mouse-tcr-v1.yaml | 19 ++++++++++++++++++- .../analyze/bd-rhapsody-mouse-tcr-v2.yaml | 19 ++++++++++++++++++- 8 files changed, 144 insertions(+), 8 deletions(-) diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml index 2ef2751b2..488dc993b 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml @@ -420,7 +420,24 @@ assemble: requiredSequences: [] inferMinRecordsPerConsensus: true assembleContigs: null -exportAlignments: null +exportAlignments: + chains: ALL + noHeader: false + fields: + - field: -readIds + - field: -targetSequences + - field: -targetQualities + - field: -vHitsWithScore + - field: -dHitsWithScore + - field: -jHitsWithScore + - field: -cHitsWithScore + - field: -vAlignments + - field: -dAlignments + - field: -jAlignments + - field: -cAlignments + - field: -allNFeaturesWithMinQuality + - field: -allAAFeatures + - field: -defaultAnchorPoints exportClones: splitByTagType: null filterOutOfFrames: false diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml index b28f6e15b..50839cc4e 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml @@ -423,7 +423,24 @@ assemble: requiredSequences: [] inferMinRecordsPerConsensus: true assembleContigs: null -exportAlignments: null +exportAlignments: + chains: ALL + noHeader: false + fields: + - field: -readIds + - field: -targetSequences + - field: -targetQualities + - field: -vHitsWithScore + - field: -dHitsWithScore + - field: -jHitsWithScore + - field: -cHitsWithScore + - field: -vAlignments + - field: -dAlignments + - field: -jAlignments + - field: -cAlignments + - field: -allNFeaturesWithMinQuality + - field: -allAAFeatures + - field: -defaultAnchorPoints exportClones: splitByTagType: null filterOutOfFrames: false diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml index 506079aaf..c9c884eb7 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml @@ -417,7 +417,24 @@ assemble: requiredSequences: [] inferMinRecordsPerConsensus: true assembleContigs: null -exportAlignments: null +exportAlignments: + chains: ALL + noHeader: false + fields: + - field: -readIds + - field: -targetSequences + - field: -targetQualities + - field: -vHitsWithScore + - field: -dHitsWithScore + - field: -jHitsWithScore + - field: -cHitsWithScore + - field: -vAlignments + - field: -dAlignments + - field: -jAlignments + - field: -cAlignments + - field: -allNFeaturesWithMinQuality + - field: -allAAFeatures + - field: -defaultAnchorPoints exportClones: splitByTagType: null filterOutOfFrames: false diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml index 2d8f6df5f..48da56d53 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml @@ -420,7 +420,24 @@ assemble: requiredSequences: [] inferMinRecordsPerConsensus: true assembleContigs: null -exportAlignments: null +exportAlignments: + chains: ALL + noHeader: false + fields: + - field: -readIds + - field: -targetSequences + - field: -targetQualities + - field: -vHitsWithScore + - field: -dHitsWithScore + - field: -jHitsWithScore + - field: -cHitsWithScore + - field: -vAlignments + - field: -dAlignments + - field: -jAlignments + - field: -cAlignments + - field: -allNFeaturesWithMinQuality + - field: -allAAFeatures + - field: -defaultAnchorPoints exportClones: splitByTagType: null filterOutOfFrames: false diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml index 9f41a0108..39e18cb85 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml @@ -424,7 +424,24 @@ assemble: requiredSequences: [] inferMinRecordsPerConsensus: true assembleContigs: null -exportAlignments: null +exportAlignments: + chains: ALL + noHeader: false + fields: + - field: -readIds + - field: -targetSequences + - field: -targetQualities + - field: -vHitsWithScore + - field: -dHitsWithScore + - field: -jHitsWithScore + - field: -cHitsWithScore + - field: -vAlignments + - field: -dAlignments + - field: -jAlignments + - field: -cAlignments + - field: -allNFeaturesWithMinQuality + - field: -allAAFeatures + - field: -defaultAnchorPoints exportClones: splitByTagType: null filterOutOfFrames: false diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml index 4fe1ecfb6..f51ef8df0 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml @@ -427,7 +427,24 @@ assemble: requiredSequences: [] inferMinRecordsPerConsensus: true assembleContigs: null -exportAlignments: null +exportAlignments: + chains: ALL + noHeader: false + fields: + - field: -readIds + - field: -targetSequences + - field: -targetQualities + - field: -vHitsWithScore + - field: -dHitsWithScore + - field: -jHitsWithScore + - field: -cHitsWithScore + - field: -vAlignments + - field: -dAlignments + - field: -jAlignments + - field: -cAlignments + - field: -allNFeaturesWithMinQuality + - field: -allAAFeatures + - field: -defaultAnchorPoints exportClones: splitByTagType: null filterOutOfFrames: false diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml index 2bf71aad5..658fb9178 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml @@ -418,7 +418,24 @@ assemble: requiredSequences: [] inferMinRecordsPerConsensus: true assembleContigs: null -exportAlignments: null +exportAlignments: + chains: ALL + noHeader: false + fields: + - field: -readIds + - field: -targetSequences + - field: -targetQualities + - field: -vHitsWithScore + - field: -dHitsWithScore + - field: -jHitsWithScore + - field: -cHitsWithScore + - field: -vAlignments + - field: -dAlignments + - field: -jAlignments + - field: -cAlignments + - field: -allNFeaturesWithMinQuality + - field: -allAAFeatures + - field: -defaultAnchorPoints exportClones: splitByTagType: null filterOutOfFrames: false diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml index 988f75143..5d2a439ec 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml @@ -421,7 +421,24 @@ assemble: requiredSequences: [] inferMinRecordsPerConsensus: true assembleContigs: null -exportAlignments: null +exportAlignments: + chains: ALL + noHeader: false + fields: + - field: -readIds + - field: -targetSequences + - field: -targetQualities + - field: -vHitsWithScore + - field: -dHitsWithScore + - field: -jHitsWithScore + - field: -cHitsWithScore + - field: -vAlignments + - field: -dAlignments + - field: -jAlignments + - field: -cAlignments + - field: -allNFeaturesWithMinQuality + - field: -allAAFeatures + - field: -defaultAnchorPoints exportClones: splitByTagType: null filterOutOfFrames: false