Merge branch 'hotfix/v1.7.2'

Author: dbolotin

CHANGELOG

@@ -1,4 +1,11 @@
 
+MiXCR 1.7.2 ( 5 May 2016)
+========================
+
+-- Fixed bug leading to mis-filtering of certain combinations of Alpha-Delta-V genes with Alpha-J 
+   or Delta-J genes
+
+
 MiXCR 1.7.1 ( 9 Mar 2016)
 ========================
 

pom.xml

@@ -32,7 +32,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>1.7.1</version>
+    <version>1.7.2</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 

src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java

@@ -103,13 +103,24 @@ public NSequenceWithQuality[] getOriginalSequences() {
     public final boolean hasSameVJLoci(final int top) {
         VDJCHit[] vHits = hits.get(GeneType.Variable),
                 jHits = hits.get(GeneType.Joining);
-        for (int v = 0; v < top && v < vHits.length; ++v)
-            for (int j = 0; j < top && j < jHits.length; ++j)
+        for (int v = 0; v < actualTop(vHits, top); ++v)
+            for (int j = 0; j < actualTop(jHits, top); ++j)
                 if (vHits[v].getAllele().getLocus() == jHits[j].getAllele().getLocus())
                     return true;
         return false;
     }
 
+    private static int actualTop(VDJCHit[] hits, int top) {
+        if (hits.length <= top)
+            return hits.length;
+        float score = hits[top].getScore() - Float.MIN_VALUE;
+        while (top < hits.length &&
+                hits[top].getScore() >= score) {
+            ++top;
+        }
+        return top;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;