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Off-by-one error in sliding window manifests itself at end of a coverage region dropping the last covered base.

This commit is contained in:
Eric Banks 2012-09-21 17:22:30 -04:00
parent 2c3dc291c0
commit 21251c29c2
2 changed files with 2 additions and 2 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
View File

@ -263,7 +263,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
if (debugLevel == 1) if (debugLevel == 1)
System.out.printf("\nOriginal: %s %s %d %d\n", read, read.getCigar(), read.getAlignmentStart(), read.getAlignmentEnd()); 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 // 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_START_SHIFT, read.getAlignmentStart());
read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT, read.getAlignmentEnd()); read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT, read.getAlignmentEnd());

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -612,7 +612,7 @@ public class SlidingWindow {
finalizedReads = closeVariantRegions(regions, true); finalizedReads = closeVariantRegions(regions, true);
if (!windowHeader.isEmpty()) { 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 finalizedReads.addAll(finalizeAndAdd(ConsensusType.BOTH)); // if it ended in running consensus, finish it up
} }