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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-04-17 17:00:14 -04:00
parent cf705f6c62 4ced094160
commit 952280bef1
1 changed files with 4 additions and 0 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
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@ -146,6 +146,10 @@ public class ConsensusAlleleCounter {
String indelString = p.getEventBases(); String indelString = p.getEventBases();
if ( p.isBeforeInsertion() ) { if ( p.isBeforeInsertion() ) {
// edge case: ignore a deletion immediately preceding an insertion as p.getEventBases() returns null [EB]
if ( indelString == null )
continue;
boolean foundKey = false; boolean foundKey = false;
// copy of hashmap into temp arrayList // copy of hashmap into temp arrayList
ArrayList<Pair<String,Integer>> cList = new ArrayList<Pair<String,Integer>>(); ArrayList<Pair<String,Integer>> cList = new ArrayList<Pair<String,Integer>>();