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Forgot to remove debugging code 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2854 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-02-18 18:12:58 +00:00
parent cc3c18d3e1
commit bbbad79f8c
1 changed files with 2 additions and 8 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -478,18 +478,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
while ( iter.hasNext() ) {
Consensus consensus = iter.next();
int indelSize = 0;
for ( CigarElement ce : consensus.cigar.getCigarElements() )
if ( ce.getOperator() == CigarOperator.I || ce.getOperator() == CigarOperator.D ) {
indelSize = ce.getLength();
break;
}
// if ( debugOn ) System.out.println("Consensus: "+consensus.str);
for ( int j = 0; j < altReads.size(); j++ ) {
AlignedRead toTest = altReads.get(j);
Pair<Integer, Integer> altAlignment = findBestOffset(consensus.str, toTest, (int)leftmostIndex, indelSize);
Pair<Integer, Integer> altAlignment = findBestOffset(consensus.str, toTest, (int)leftmostIndex);
// the mismatch score is the min of its alignment vs. the reference and vs. the alternate
int myScore = altAlignment.second;
@ -695,7 +689,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
return new Consensus(altConsensus, cigar, indexOnRef);
}
private Pair<Integer, Integer> findBestOffset(final byte[] ref, final AlignedRead read, final int leftmostIndex, int indelSize) {
private Pair<Integer, Integer> findBestOffset(final byte[] ref, final AlignedRead read, final int leftmostIndex) {
// optimization: try the most likely alignment first (to get a low score to beat)
int originalAlignment = read.getOriginalAlignmentStart() - leftmostIndex;