Make chimeric read filter optional

Author: julianhess

src/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTect.java

@@ -791,7 +791,7 @@ private LocusReadPile filterReads(final ReferenceContext ref, final ReadBackedPi
 
             // is this a discordant read pair?
             // TODO: add option to disable this filter
-            if(read.getMateReferenceIndex() != read.getReferenceIndex()) {
+            if(MTAC.EXCLUDE_CHIMERIC_READS && read.getMateReferenceIndex() != read.getReferenceIndex()) {
                 continue;
             }
 

src/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTectArgumentCollection.java

@@ -130,6 +130,9 @@ public class MuTectArgumentCollection {
     @Argument(fullName = "heavily_clipped_read_fraction", required = false, doc = "if this fraction or more of the bases in a read are soft/hard clipped, do not use this read for mutation calling")
     public float HEAVILY_CLIPPED_READ_FRACTION = 0.30f;
 
+    @Argument(fullName = "exclude_chimeric_reads", required = false, doc = "exclude chimeric reads from processing")
+    public boolean EXCLUDE_CHIMERIC_READS = false;
+
     @Argument(fullName = "fraction_mapq0_threshold", required = false, doc = "threshold for determining if there is relatedness between the alt and ref allele read piles")
     public float FRACTION_MAPQ0_THRESHOLD = 0.5f;