This allows alignment attached features in mutation export fields.

This fixes #301
milaboratory · Dec 12, 2017 · 59b4d89 · 59b4d89
1 parent 00cd0ba
commit 59b4d89
Show file tree

Hide file tree

Showing 4 changed files with 9 additions and 5 deletions.
diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT
@@ -1 +1,2 @@
+Now export fields like `-nMutationsRelative` supports alignment-attached gene features (e.g. this allows to export all mutations of V gene inside CDR3 region: `-nMutationsRelative VCDR3Part VRegionWithP`)
 minor: `--noMerge` option renamed to `--no-merge` in assemble action
diff --git a/pom.xml b/pom.xml
@@ -32,7 +32,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>2.1.8-SNAPSHOT</version>
+    <version>2.2-SNAPSHOT</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 
@@ -44,14 +44,14 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <milib.version>1.8.1</milib.version>
+        <milib.version>1.8.2-SNAPSHOT</milib.version>
     </properties>
 
     <dependencies>
         <dependency>
             <groupId>io.repseq</groupId>
             <artifactId>repseqio</artifactId>
-            <version>1.2.10</version>
+            <version>1.2.11-SNAPSHOT</version>
         </dependency>
 
         <dependency>

diff --git a/repseqio b/repseqio
diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
@@ -119,7 +119,10 @@ protected String extractValue(VDJCObject object, GeneFeature[] parameters) {
             if (!germlinePartitioning.isAvailable(bigGeneFeature))
                 return "-";
 
-            Range smallTargetRage = germlinePartitioning.getRelativeRange(alignedFeature, smallGeneFeature);
+            Range smallTargetRage =
+                    smallGeneFeature.isAlignmentAttached() ?
+                            null :
+                            germlinePartitioning.getRelativeRange(alignedFeature, smallGeneFeature);
             if (smallTargetRage == null)
                 for (int i = 0; i < object.numberOfTargets(); i++) {
                     SequencePartitioning pt = object.getPartitionedTarget(i).getPartitioning();