Merge pull request #1282 from milaboratory/mixcr-regression-tests/ont…

…-aligner-parameters Regression tests changes in the ont-aligner-parameters
milaboratory · Jul 29, 2023 · d12d914 · d12d914
2 parents a1e13d7 + 6e20d16
commit d12d914
Show file tree

Hide file tree

Showing 3 changed files with 30 additions and 30 deletions.
diff --git a/regression/presets/analyze/flairr-seq-bcr.yaml b/regression/presets/analyze/flairr-seq-bcr.yaml
@@ -77,27 +77,27 @@ align:
       relativeMinScore: 0.97
       parameters:
         type: kaligner2
-        mapperNValue: 12
+        mapperNValue: 10
         mapperKValue: 1
         floatingLeftBound: true
         floatingRightBound: false
-        mapperAbsoluteMinClusterScore: 102
+        mapperAbsoluteMinClusterScore: 130
         mapperExtraClusterScore: -38
-        mapperMatchScore: 134
+        mapperMatchScore: 93
         mapperMismatchScore: -14
         mapperOffsetShiftScore: -82
-        mapperSlotCount: 11
-        mapperMaxClusters: 12
+        mapperSlotCount: 7
+        mapperMaxClusters: 4
         mapperMaxClusterIndels: 4
         mapperKMersPerPosition: 4
-        mapperAbsoluteMinScore: 100
-        mapperRelativeMinScore: 0.94
-        mapperMinSeedsDistance: 6
-        mapperMaxSeedsDistance: 8
+        mapperAbsoluteMinScore: 130
+        mapperRelativeMinScore: 0.77
+        mapperMinSeedsDistance: 5
+        mapperMaxSeedsDistance: 5
         alignmentStopPenalty: 0
         absoluteMinScore: 112
         relativeMinScore: 0.78
-        maxHits: 3
+        maxHits: 5
         scoring:
           type: affine
           alphabet: nucleotide

diff --git a/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml b/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml
@@ -74,27 +74,27 @@ align:
       relativeMinScore: 0.97
       parameters:
         type: kaligner2
-        mapperNValue: 12
+        mapperNValue: 10
         mapperKValue: 1
         floatingLeftBound: true
         floatingRightBound: false
-        mapperAbsoluteMinClusterScore: 102
+        mapperAbsoluteMinClusterScore: 130
         mapperExtraClusterScore: -38
-        mapperMatchScore: 134
+        mapperMatchScore: 93
         mapperMismatchScore: -14
         mapperOffsetShiftScore: -82
-        mapperSlotCount: 11
-        mapperMaxClusters: 12
+        mapperSlotCount: 7
+        mapperMaxClusters: 4
         mapperMaxClusterIndels: 4
         mapperKMersPerPosition: 4
-        mapperAbsoluteMinScore: 100
-        mapperRelativeMinScore: 0.94
-        mapperMinSeedsDistance: 6
-        mapperMaxSeedsDistance: 8
+        mapperAbsoluteMinScore: 130
+        mapperRelativeMinScore: 0.77
+        mapperMinSeedsDistance: 5
+        mapperMaxSeedsDistance: 5
         alignmentStopPenalty: 0
         absoluteMinScore: 112
         relativeMinScore: 0.78
-        maxHits: 3
+        maxHits: 5
         scoring:
           type: affine
           alphabet: nucleotide

diff --git a/regression/presets/analyze/ont-rna-seq.yaml b/regression/presets/analyze/ont-rna-seq.yaml
@@ -74,27 +74,27 @@ align:
       relativeMinScore: 0.97
       parameters:
         type: kaligner2
-        mapperNValue: 12
+        mapperNValue: 10
         mapperKValue: 1
         floatingLeftBound: true
         floatingRightBound: false
-        mapperAbsoluteMinClusterScore: 102
+        mapperAbsoluteMinClusterScore: 130
         mapperExtraClusterScore: -38
-        mapperMatchScore: 134
+        mapperMatchScore: 93
         mapperMismatchScore: -14
         mapperOffsetShiftScore: -82
-        mapperSlotCount: 11
-        mapperMaxClusters: 12
+        mapperSlotCount: 7
+        mapperMaxClusters: 4
         mapperMaxClusterIndels: 4
         mapperKMersPerPosition: 4
-        mapperAbsoluteMinScore: 100
-        mapperRelativeMinScore: 0.94
-        mapperMinSeedsDistance: 6
-        mapperMaxSeedsDistance: 8
+        mapperAbsoluteMinScore: 130
+        mapperRelativeMinScore: 0.77
+        mapperMinSeedsDistance: 5
+        mapperMaxSeedsDistance: 5
         alignmentStopPenalty: 0
         absoluteMinScore: 112
         relativeMinScore: 0.78
-        maxHits: 3
+        maxHits: 5
         scoring:
           type: affine
           alphabet: nucleotide