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RR bug: we were adding synthetic reads from the header only before the variant region, which meant that reads that overlap the variant region but that weren't used for the consensus (because e.g. of low base quality for the spanning base) were never being used at all. Instead, add synthetic reads from before and spanning the variant region.

This commit is contained in:
Eric Banks 2012-09-24 13:29:37 -04:00
parent ef680e1e13
commit 6a73265a06
1 changed files with 1 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -546,7 +546,7 @@ public class SlidingWindow {
List<GATKSAMRecord> allReads = compressVariantRegion(start, stop);
List<GATKSAMRecord> result = (downsampleCoverage > 0) ? downsampleVariantRegion(allReads) : allReads;
result.addAll(addToSyntheticReads(windowHeader, 0, start, false));
result.addAll(addToSyntheticReads(windowHeader, 0, stop, false));
result.addAll(finalizeAndAdd(ConsensusType.BOTH));
return result; // finalized reads will be downsampled if necessary