Support of different quality merging algorithms.

milaboratory · Sep 17, 2015 · 74e4972 · 74e4972
1 parent d4bd460
commit 74e4972
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Showing 9 changed files with 14 additions and 147 deletions.
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,5 @@ target
 *.iml
 .idea
 doc/_build
+.floo
+.flooignore
diff --git a/pom.xml b/pom.xml
@@ -44,7 +44,7 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <milib.version>1.1.1</milib.version>
+        <milib.version>1.1.2-SNAPSHOT</milib.version>
     </properties>
 
     <dependencies>

diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/PairedEndReadsLayout.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/PairedEndReadsLayout.java
diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/PairedTarget.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/PairedTarget.java
diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerPVFirst.java
@@ -28,6 +28,7 @@
  */
 package com.milaboratory.mixcr.vdjaligners;
 
+import com.milaboratory.core.PairedTarget;
 import com.milaboratory.core.Range;
 import com.milaboratory.core.alignment.Alignment;
 import com.milaboratory.core.alignment.AlignmentUtils;

diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java
@@ -33,6 +33,7 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+import com.milaboratory.core.PairedEndReadsLayout;
 import com.milaboratory.mitools.merger.MergerParameters;
 import com.milaboratory.mixcr.basictypes.HasFeatureToAlign;
 import com.milaboratory.mixcr.reference.Allele;

diff --git a/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java b/src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerWithMerge.java
@@ -48,8 +48,9 @@ public VDJCAlignerWithMerge(VDJCAlignerParameters parameters) {
         super(parameters);
         singleAligner = new VDJCAlignerSJFirst(parameters);
         pairedAligner = new VDJCAlignerPVFirst(parameters);
-        merger = new MismatchOnlyPairedReadMerger(parameters.getMergerParameters(),
-                parameters.getReadsLayout().isOpposite());
+        merger = new MismatchOnlyPairedReadMerger(
+                parameters.getMergerParameters().overrideReadsLayout(
+                        parameters.getReadsLayout()));
     }
 
     @Override

diff --git a/src/main/resources/parameters/vdjcaligner_parameters.json b/src/main/resources/parameters/vdjcaligner_parameters.json
@@ -93,6 +93,7 @@
         "includeDScore": false,
         "includeCScore": false,
         "mergerParameters": {
+            "qualityMergingAlgorithm" : "SumSubtraction",
             "minimalOverlap": 17,
             "minimalIdentity": 0.9
         },
@@ -196,6 +197,7 @@
         "includeDScore": true,
         "includeCScore": true,
         "mergerParameters": {
+            "qualityMergingAlgorithm" : "SumSubtraction",
             "minimalOverlap": 17,
             "minimalIdentity": 0.9
         },

diff --git a/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java b/src/test/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParametersTest.java
@@ -28,10 +28,12 @@
  */
 package com.milaboratory.mixcr.vdjaligners;
 
+import com.milaboratory.core.PairedEndReadsLayout;
 import com.milaboratory.core.alignment.AffineGapAlignmentScoring;
 import com.milaboratory.core.alignment.KAlignerParameters;
 import com.milaboratory.core.alignment.LinearGapAlignmentScoring;
 import com.milaboratory.mitools.merger.MergerParameters;
+import com.milaboratory.mitools.merger.QualityMergingAlgorithm;
 import com.milaboratory.mixcr.reference.GeneFeature;
 import com.milaboratory.mixcr.reference.LociLibrary;
 import com.milaboratory.mixcr.reference.LociLibraryManager;
@@ -61,7 +63,8 @@ public void test1() throws Exception {
                                 LinearGapAlignmentScoring.getNucleotideBLASTScoring())),
                 VJAlignmentOrder.JThenV,
                 false, false,
-                120.0f, 5, 0.7f, 0.7f, PairedEndReadsLayout.Opposite, new MergerParameters(12, 0.12));
+                120.0f, 5, 0.7f, 0.7f, PairedEndReadsLayout.Opposite, new MergerParameters(
+                QualityMergingAlgorithm.SumSubtraction, null, 12, 0.12));
         String str = GlobalObjectMappers.PRETTY.writeValueAsString(paramentrs);
         VDJCAlignerParameters deser = GlobalObjectMappers.PRETTY.readValue(str, VDJCAlignerParameters.class);
         assertEquals(paramentrs, deser);