From 21251c29c2fd74fcbb4af56ebdeeeb85be4f43a0 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 21 Sep 2012 17:22:30 -0400 Subject: [PATCH] Off-by-one error in sliding window manifests itself at end of a coverage region dropping the last covered base. --- .../sting/gatk/walkers/compression/reducereads/ReduceReads.java | 2 +- .../gatk/walkers/compression/reducereads/SlidingWindow.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index 0def4e582..1beee3cbe 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -263,7 +263,7 @@ public class ReduceReads extends ReadWalker, ReduceRea if (debugLevel == 1) System.out.printf("\nOriginal: %s %s %d %d\n", read, read.getCigar(), read.getAlignmentStart(), read.getAlignmentEnd()); - // we write the actual alignment starts to their respectiv alignment shift tags in the temporary + // we write the actual alignment starts to their respective alignment shift tags in the temporary // attribute hash so we can determine later if we need to write down the alignment shift to the reduced BAM file read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT, read.getAlignmentStart()); read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT, read.getAlignmentEnd()); 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 5820dc5f5..b486905e6 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 @@ -612,7 +612,7 @@ public class SlidingWindow { finalizedReads = closeVariantRegions(regions, true); if (!windowHeader.isEmpty()) { - finalizedReads.addAll(addToSyntheticReads(windowHeader, 0, windowHeader.size() - 1, false)); + finalizedReads.addAll(addToSyntheticReads(windowHeader, 0, windowHeader.size(), false)); finalizedReads.addAll(finalizeAndAdd(ConsensusType.BOTH)); // if it ended in running consensus, finish it up }