From 6a73265a06e75e1c63447f7318834c4b9fb36aad Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 24 Sep 2012 13:29:37 -0400 Subject: [PATCH] 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. --- .../gatk/walkers/compression/reducereads/SlidingWindow.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 d55560a70..6d6cbce04 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 @@ -546,7 +546,7 @@ public class SlidingWindow { List allReads = compressVariantRegion(start, stop); List 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