Unfortunately, because BWA occasionally outputs crazy reads, we need

to make sure not to have an ArrayIndexOutOfBoundsException thrown.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@297 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java

@@ -37,10 +37,12 @@ public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
 
             int start = read.getAlignmentStart()-1;
             int stop  = read.getAlignmentEnd();
+            // sometimes BWA outputs screwy reads
+            if ( stop >= context.getReferenceContig().getBases().length )
+                return 0;
 
             List<Byte> refSeq = Utils.subseq(context.getReferenceContig().getBases(), start, stop);
             List<Byte> readBases = Utils.subseq(read.getReadBases());
-
             assert(refSeq.size() == readBases.size());
 
             // it's actually faster to reallocate a resized array than to use ArrayLists...

java/src/org/broadinstitute/sting/utils/Utils.java

@@ -163,6 +163,7 @@ public class Utils {
     }
 
     public static ArrayList<Byte> subseq(byte[] fullArray, int start, int end) {
+        assert end < fullArray.length;
         ArrayList<Byte> dest = new ArrayList<Byte>(end - start + 1);
         for (int i = start; i < end; i++) {
             dest.add(fullArray[i]);