From ff391078c75188e235565702f34076190114083a Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Wed, 29 Nov 2023 15:31:06 +0100 Subject: [PATCH 1/4] chore: mitool upgrade --- build.gradle.kts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 14eaee857..3b91a7c7a 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -134,13 +134,13 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.5.0-114-export-changes" +val mixcrAlgoVersion = "4.5.0-115-develop" // may be blank (will be inherited from mixcr-algo) val milibVersion = "" // may be blank (will be inherited from mixcr-algo or milib) val miuVersion = "" // may be blank (will be inherited from mixcr-algo) -val mitoolVersion = "" +val mitoolVersion = "2.1.0-5-main" // may be blank (will be inherited from mixcr-algo) val repseqioVersion = "2.3.0-8-fix-geneFeatures-parse" From 59743e9f19ed895ea7d69432fc1b2f62aeefe030 Mon Sep 17 00:00:00 2001 From: Alex Davydov Date: Wed, 29 Nov 2023 18:49:20 +0100 Subject: [PATCH 2/4] kmer filter minBinWidth=6 --- src/main/resources/presets/protocols/10x.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/resources/presets/protocols/10x.yaml b/src/main/resources/presets/protocols/10x.yaml index e05bb9799..9ce51c8e0 100644 --- a/src/main/resources/presets/protocols/10x.yaml +++ b/src/main/resources/presets/protocols/10x.yaml @@ -90,7 +90,8 @@ topShare: 0.7 minSequenceCount: 4 reportHist: - binNumber: 40 + binNumber: 0 + minBinWidth: 6 operator: type: group_operator_range lower: 150.0 From debdfe693282034463f0cc39952594c727b3752f Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Thu, 30 Nov 2023 15:37:36 +0100 Subject: [PATCH 3/4] chore: mitool upgrade, text fix --- build.gradle.kts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle.kts b/build.gradle.kts index 3b91a7c7a..9f2709a16 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -140,7 +140,7 @@ val milibVersion = "" // may be blank (will be inherited from mixcr-algo or milib) val miuVersion = "" // may be blank (will be inherited from mixcr-algo) -val mitoolVersion = "2.1.0-5-main" +val mitoolVersion = "2.1.0-6-main" // may be blank (will be inherited from mixcr-algo) val repseqioVersion = "2.3.0-8-fix-geneFeatures-parse" From 5a0d3e7356a17e1efca9fc82236553611994b0c6 Mon Sep 17 00:00:00 2001 From: dbolotin Date: Thu, 30 Nov 2023 14:47:28 +0000 Subject: [PATCH 4/4] regression tests automated change --- .../presets/analyze/10x-sc-xcr-vdj.yaml | 4 +- .../analyze/10x-vdj-bcr-full-length.yaml | 4 +- regression/presets/analyze/10x-vdj-bcr.yaml | 4 +- .../10x-vdj-tcr-alias-multi-barcode-test.yaml | 4 +- .../analyze/10x-vdj-tcr-full-length.yaml | 4 +- .../presets/analyze/10x-vdj-tcr-qc-test.yaml | 4 +- regression/presets/analyze/10x-vdj-tcr.yaml | 4 +- regression/reports/baseSingleCell.raw.yaml | 170 +++++++++--------- .../reports/baseSingleCell.vdjcontigs.yaml | 170 +++++++++--------- 9 files changed, 184 insertions(+), 184 deletions(-) diff --git a/regression/presets/analyze/10x-sc-xcr-vdj.yaml b/regression/presets/analyze/10x-sc-xcr-vdj.yaml index a485a6936..f1f32f9a9 100644 --- a/regression/presets/analyze/10x-sc-xcr-vdj.yaml +++ b/regression/presets/analyze/10x-sc-xcr-vdj.yaml @@ -263,8 +263,8 @@ refineTagsAndSort: minSequenceCount: 4 reportHist: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false operator: type: group_operator_range diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml index a00d96e91..72801aa9b 100644 --- a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml @@ -263,8 +263,8 @@ refineTagsAndSort: minSequenceCount: 4 reportHist: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false operator: type: group_operator_range diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml index a485a6936..f1f32f9a9 100644 --- a/regression/presets/analyze/10x-vdj-bcr.yaml +++ b/regression/presets/analyze/10x-vdj-bcr.yaml @@ -263,8 +263,8 @@ refineTagsAndSort: minSequenceCount: 4 reportHist: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false operator: type: group_operator_range 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 235f0da69..763c6bb94 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 @@ -263,8 +263,8 @@ refineTagsAndSort: minSequenceCount: 4 reportHist: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false operator: type: group_operator_range diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml index a00d96e91..72801aa9b 100644 --- a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml @@ -263,8 +263,8 @@ refineTagsAndSort: minSequenceCount: 4 reportHist: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false operator: type: group_operator_range diff --git a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml index 3bce2658d..10029ccb9 100644 --- a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml @@ -265,8 +265,8 @@ refineTagsAndSort: minSequenceCount: 4 reportHist: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false operator: type: group_operator_range diff --git a/regression/presets/analyze/10x-vdj-tcr.yaml b/regression/presets/analyze/10x-vdj-tcr.yaml index a485a6936..f1f32f9a9 100644 --- a/regression/presets/analyze/10x-vdj-tcr.yaml +++ b/regression/presets/analyze/10x-vdj-tcr.yaml @@ -263,8 +263,8 @@ refineTagsAndSort: minSequenceCount: 4 reportHist: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false operator: type: group_operator_range diff --git a/regression/reports/baseSingleCell.raw.yaml b/regression/reports/baseSingleCell.raw.yaml index 035eb1ea0..ab7a9536a 100644 --- a/regression/reports/baseSingleCell.raw.yaml +++ b/regression/reports/baseSingleCell.raw.yaml @@ -480,127 +480,127 @@ refineTagsAndSort: metricHists: - bins: - from: 56.0 - to: 61.925 + to: 62.0 weight: 25.0 - - from: 61.925 - to: 67.85 + - from: 62.0 + to: 68.0 weight: 1.0 - - from: 67.85 - to: 73.775 + - from: 68.0 + to: 74.0 weight: 1.0 - - from: 73.775 - to: 79.7 + - from: 74.0 + to: 80.0 weight: 0.0 - - from: 79.7 - to: 85.625 + - from: 80.0 + to: 86.0 weight: 0.0 - - from: 85.625 - to: 91.55 + - from: 86.0 + to: 92.0 weight: 0.0 - - from: 91.55 - to: 97.475 + - from: 92.0 + to: 98.0 weight: 0.0 - - from: 97.475 - to: 103.4 + - from: 98.0 + to: 104.0 weight: 0.0 - - from: 103.4 - to: 109.32499999999999 + - from: 104.0 + to: 110.0 weight: 0.0 - - from: 109.32499999999999 - to: 115.25 + - from: 110.0 + to: 116.0 weight: 0.0 - - from: 115.25 - to: 121.175 + - from: 116.0 + to: 122.0 weight: 0.0 - - from: 121.175 - to: 127.1 + - from: 122.0 + to: 128.0 weight: 0.0 - - from: 127.1 - to: 133.02499999999998 + - from: 128.0 + to: 134.0 weight: 0.0 - - from: 133.02499999999998 - to: 138.95 + - from: 134.0 + to: 140.0 weight: 0.0 - - from: 138.95 - to: 144.875 + - from: 140.0 + to: 146.0 weight: 0.0 - - from: 144.875 - to: 150.8 + - from: 146.0 + to: 152.0 weight: 0.0 - - from: 150.8 - to: 156.725 + - from: 152.0 + to: 158.0 weight: 1.0 - - from: 156.725 - to: 162.64999999999998 + - from: 158.0 + to: 164.0 weight: 0.0 - - from: 162.64999999999998 - to: 168.575 + - from: 164.0 + to: 170.0 weight: 0.0 - - from: 168.575 - to: 174.5 + - from: 170.0 + to: 176.0 weight: 0.0 - - from: 174.5 - to: 180.425 + - from: 176.0 + to: 182.0 weight: 1.0 - - from: 180.425 - to: 186.35 + - from: 182.0 + to: 188.0 weight: 0.0 - - from: 186.35 - to: 192.275 + - from: 188.0 + to: 194.0 weight: 0.0 - - from: 192.275 - to: 198.2 + - from: 194.0 + to: 200.0 weight: 0.0 - - from: 198.2 - to: 204.125 + - from: 200.0 + to: 206.0 weight: 0.0 - - from: 204.125 - to: 210.04999999999998 + - from: 206.0 + to: 212.0 weight: 0.0 - - from: 210.04999999999998 - to: 215.975 + - from: 212.0 + to: 218.0 weight: 3.0 - - from: 215.975 - to: 221.9 - weight: 1.0 - - from: 221.9 - to: 227.825 + - from: 218.0 + to: 224.0 weight: 2.0 - - from: 227.825 - to: 233.75 - weight: 6.0 - - from: 233.75 - to: 239.67499999999998 + - from: 224.0 + to: 230.0 + weight: 2.0 + - from: 230.0 + to: 236.0 + weight: 8.0 + - from: 236.0 + to: 242.0 weight: 10.0 - - from: 239.67499999999998 - to: 245.6 + - from: 242.0 + to: 248.0 + weight: 8.0 + - from: 248.0 + to: 254.0 + weight: 12.0 + - from: 254.0 + to: 260.0 weight: 7.0 - - from: 245.6 - to: 251.525 - weight: 10.0 - - from: 251.525 - to: 257.45 - weight: 13.0 - - from: 257.45 - to: 263.375 + - from: 260.0 + to: 266.0 weight: 6.0 - - from: 263.375 - to: 269.29999999999995 + - from: 266.0 + to: 272.0 weight: 1.0 - - from: 269.29999999999995 - to: 275.225 + - from: 272.0 + to: 278.0 weight: 0.0 - - from: 275.225 - to: 281.15 + - from: 278.0 + to: 284.0 weight: 0.0 - - from: 281.15 - to: 287.075 + - from: 284.0 + to: 290.0 weight: 0.0 - - from: 287.075 - to: 293.0 + - from: 290.0 + to: 296.0 weight: 1.0 collectionSpec: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false diff --git a/regression/reports/baseSingleCell.vdjcontigs.yaml b/regression/reports/baseSingleCell.vdjcontigs.yaml index 83cdbb964..617fd43e3 100644 --- a/regression/reports/baseSingleCell.vdjcontigs.yaml +++ b/regression/reports/baseSingleCell.vdjcontigs.yaml @@ -483,127 +483,127 @@ refineTagsAndSort: metricHists: - bins: - from: 56.0 - to: 61.925 + to: 62.0 weight: 25.0 - - from: 61.925 - to: 67.85 + - from: 62.0 + to: 68.0 weight: 1.0 - - from: 67.85 - to: 73.775 + - from: 68.0 + to: 74.0 weight: 1.0 - - from: 73.775 - to: 79.7 + - from: 74.0 + to: 80.0 weight: 0.0 - - from: 79.7 - to: 85.625 + - from: 80.0 + to: 86.0 weight: 0.0 - - from: 85.625 - to: 91.55 + - from: 86.0 + to: 92.0 weight: 0.0 - - from: 91.55 - to: 97.475 + - from: 92.0 + to: 98.0 weight: 0.0 - - from: 97.475 - to: 103.4 + - from: 98.0 + to: 104.0 weight: 0.0 - - from: 103.4 - to: 109.32499999999999 + - from: 104.0 + to: 110.0 weight: 0.0 - - from: 109.32499999999999 - to: 115.25 + - from: 110.0 + to: 116.0 weight: 0.0 - - from: 115.25 - to: 121.175 + - from: 116.0 + to: 122.0 weight: 0.0 - - from: 121.175 - to: 127.1 + - from: 122.0 + to: 128.0 weight: 0.0 - - from: 127.1 - to: 133.02499999999998 + - from: 128.0 + to: 134.0 weight: 0.0 - - from: 133.02499999999998 - to: 138.95 + - from: 134.0 + to: 140.0 weight: 0.0 - - from: 138.95 - to: 144.875 + - from: 140.0 + to: 146.0 weight: 0.0 - - from: 144.875 - to: 150.8 + - from: 146.0 + to: 152.0 weight: 0.0 - - from: 150.8 - to: 156.725 + - from: 152.0 + to: 158.0 weight: 1.0 - - from: 156.725 - to: 162.64999999999998 + - from: 158.0 + to: 164.0 weight: 0.0 - - from: 162.64999999999998 - to: 168.575 + - from: 164.0 + to: 170.0 weight: 0.0 - - from: 168.575 - to: 174.5 + - from: 170.0 + to: 176.0 weight: 0.0 - - from: 174.5 - to: 180.425 + - from: 176.0 + to: 182.0 weight: 1.0 - - from: 180.425 - to: 186.35 + - from: 182.0 + to: 188.0 weight: 0.0 - - from: 186.35 - to: 192.275 + - from: 188.0 + to: 194.0 weight: 0.0 - - from: 192.275 - to: 198.2 + - from: 194.0 + to: 200.0 weight: 0.0 - - from: 198.2 - to: 204.125 + - from: 200.0 + to: 206.0 weight: 0.0 - - from: 204.125 - to: 210.04999999999998 + - from: 206.0 + to: 212.0 weight: 0.0 - - from: 210.04999999999998 - to: 215.975 + - from: 212.0 + to: 218.0 weight: 3.0 - - from: 215.975 - to: 221.9 - weight: 1.0 - - from: 221.9 - to: 227.825 + - from: 218.0 + to: 224.0 weight: 2.0 - - from: 227.825 - to: 233.75 - weight: 6.0 - - from: 233.75 - to: 239.67499999999998 + - from: 224.0 + to: 230.0 + weight: 2.0 + - from: 230.0 + to: 236.0 + weight: 8.0 + - from: 236.0 + to: 242.0 weight: 10.0 - - from: 239.67499999999998 - to: 245.6 + - from: 242.0 + to: 248.0 + weight: 8.0 + - from: 248.0 + to: 254.0 + weight: 12.0 + - from: 254.0 + to: 260.0 weight: 7.0 - - from: 245.6 - to: 251.525 - weight: 10.0 - - from: 251.525 - to: 257.45 - weight: 13.0 - - from: 257.45 - to: 263.375 + - from: 260.0 + to: 266.0 weight: 6.0 - - from: 263.375 - to: 269.29999999999995 + - from: 266.0 + to: 272.0 weight: 1.0 - - from: 269.29999999999995 - to: 275.225 + - from: 272.0 + to: 278.0 weight: 0.0 - - from: 275.225 - to: 281.15 + - from: 278.0 + to: 284.0 weight: 0.0 - - from: 281.15 - to: 287.075 + - from: 284.0 + to: 290.0 weight: 0.0 - - from: 287.075 - to: 293.0 + - from: 290.0 + to: 296.0 weight: 1.0 collectionSpec: log: false - binNumber: 40 - minBinWidth: 0.0 + binNumber: 0 + minBinWidth: 6.0 multiplyWeightByKey: false