diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java index 2db1e7cf9..50dd2e810 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java @@ -416,7 +416,7 @@ public class SlidingWindow { */ private void addToFilteredData(LinkedList header, int start, int end) { if (filteredDataConsensus == null) - filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, getStartLocation(header), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities); + filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, header.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities); ListIterator headerElementIterator = header.listIterator(start); for (int index = start; index < end; index++) { @@ -445,7 +445,7 @@ public class SlidingWindow { */ private void addToRunningConsensus(LinkedList header, int start, int end) { if (runningConsensus == null) - runningConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, consensusReadName + consensusCounter++, getStartLocation(header), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities); + runningConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, consensusReadName + consensusCounter++, header.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities); Iterator headerElementIterator = header.listIterator(start); for (int index = start; index < end; index++) {