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Fixing but reported by Thomas in the forum where reads were soft-clipped beyond the limits of the contig and ReduceReads was failing with a NoSuchElement exception. Now we hard clip anything that goes beyond the boundaries of the contig.

This commit is contained in:
Mauricio Carneiro 2012-08-09 15:58:18 -04:00
parent c6132ebe26
commit 67d4148b32
1 changed files with 9 additions and 2 deletions
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11
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -251,7 +251,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
LinkedList<GATKSAMRecord> mappedReads;
totalReads++;
if (!debugRead.isEmpty() && read.getReadName().contains(debugRead))
System.out.println("Found debug read!");
System.out.println("Found debug read!");
if (debugLevel == 1)
System.out.printf("\nOriginal: %s %s %d %d\n", read, read.getCigar(), read.getAlignmentStart(), read.getAlignmentEnd());
@ -260,7 +260,14 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
// 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());
// Check if the read goes beyond the boundaries of the chromosome, and hard clip those boundaries.
int chromosomeLength = ref.getGenomeLocParser().getContigInfo(read.getReferenceName()).getSequenceLength();
if (read.getSoftStart() < 0)
read = ReadClipper.hardClipByReadCoordinates(read, 0, -read.getSoftStart() - 1);
if (read.getSoftEnd() > chromosomeLength)
read = ReadClipper.hardClipByReadCoordinates(read, chromosomeLength - read.getSoftStart() + 1, read.getReadLength() - 1);
if (!DONT_SIMPLIFY_READS)
read.simplify(); // Clear all unnecessary attributes
if (!DONT_CLIP_ADAPTOR_SEQUENCES)