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Not every consensus is well aligned. Need to check more, but starting position has been fixed.

This commit is contained in:
Mauricio Carneiro 2012-08-13 17:11:12 -04:00
parent 97874b92d1
commit aa1d2f3a5b
1 changed files with 2 additions and 2 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -416,7 +416,7 @@ public class SlidingWindow {
*/ */
private void addToFilteredData(LinkedList<HeaderElement> header, int start, int end) { private void addToFilteredData(LinkedList<HeaderElement> header, int start, int end) {
if (filteredDataConsensus == null) if (filteredDataConsensus == null)
filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, windowHeader.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities); filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, getStartLocation(header), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities);
ListIterator<HeaderElement> headerElementIterator = header.listIterator(start); ListIterator<HeaderElement> headerElementIterator = header.listIterator(start);
for (int index = start; index < end; index++) { for (int index = start; index < end; index++) {
@ -445,7 +445,7 @@ public class SlidingWindow {
*/ */
private void addToRunningConsensus(LinkedList<HeaderElement> header, int start, int end) { private void addToRunningConsensus(LinkedList<HeaderElement> header, int start, int end) {
if (runningConsensus == null) if (runningConsensus == null)
runningConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, consensusReadName + consensusCounter++, windowHeader.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities); runningConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, consensusReadName + consensusCounter++, getStartLocation(header), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities);
Iterator<HeaderElement> headerElementIterator = header.listIterator(start); Iterator<HeaderElement> headerElementIterator = header.listIterator(start);
for (int index = start; index < end; index++) { for (int index = start; index < end; index++) {