From 7105ad65a6ab37a675d74cd468316f122cb3c40c Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 2 Apr 2013 15:57:45 -0400 Subject: [PATCH] Remove the capability of EventMap to emit symbolic alleles for unassembled events -- These events always occur on the very edge of the haplotypes, and are intrinsically dodgy. So instead of emitting them and then potentially having to deal with merging real basepair events into them we just no longer emit those events. --- .../org/broadinstitute/sting/utils/haplotype/EventMap.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java b/public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java index 7bc6acbfe..1d33e328d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java +++ b/public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java @@ -105,8 +105,9 @@ public class EventMap extends TreeMap { if( BaseUtils.isRegularBase(refByte) ) { insertionAlleles.add( Allele.create(refByte, true) ); } - if( cigarIndex == 0 || cigarIndex == cigar.getCigarElements().size() - 1 ) { // if the insertion isn't completely resolved in the haplotype then make it a symbolic allele - insertionAlleles.add( SYMBOLIC_UNASSEMBLED_EVENT_ALLELE ); + if( cigarIndex == 0 || cigarIndex == cigar.getCigarElements().size() - 1 ) { + // if the insertion isn't completely resolved in the haplotype, skip it + // note this used to emit SYMBOLIC_UNASSEMBLED_EVENT_ALLELE but that seems dangerous } else { byte[] insertionBases = new byte[]{}; insertionBases = ArrayUtils.add(insertionBases, ref[refPos - 1]); // add the padding base