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Fix for Ryan: don't pull reference sequence for the portions of reads that extend beyond the contig boundaries 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4551 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-22 14:38:26 +00:00
parent 9f76aed515
commit 181f901126
2 changed files with 5 additions and 5 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -453,9 +453,9 @@ public class UnifiedGenotyperEngine {
bitset.set(i); bitset.set(i);
} }
// if a read is too long for the reference context, extend the context // if a read is too long for the reference context, extend the context (being sure not to extend past the end of the chromosome)
if ( record.getAlignmentEnd() > refContext.getWindow().getStop() ) { if ( record.getAlignmentEnd() > refContext.getWindow().getStop() ) {
GenomeLoc window = GenomeLocParser.createGenomeLoc(refContext.getLocus().getContig(), refContext.getWindow().getStart(), record.getAlignmentEnd()); GenomeLoc window = GenomeLocParser.createGenomeLoc(refContext.getLocus().getContig(), refContext.getWindow().getStart(), Math.min(record.getAlignmentEnd(), referenceReader.getSequenceDictionary().getSequence(refContext.getLocus().getContig()).getSequenceLength()));
byte[] bases = referenceReader.getSubsequenceAt(window.getContig(), window.getStart(), window.getStop()).getBases(); byte[] bases = referenceReader.getSubsequenceAt(window.getContig(), window.getStart(), window.getStop()).getBases();
StringUtil.toUpperCase(bases); StringUtil.toUpperCase(bases);
refContext = new ReferenceContext(refContext.getLocus(), window, bases); refContext = new ReferenceContext(refContext.getLocus(), window, bases);

6
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -285,9 +285,9 @@ public class AlignmentUtils {
if ( currentReadPos++ < readStartPos ) if ( currentReadPos++ < readStartPos )
continue; continue;
if ( refIndex >= refBases.length ) { // this is possible if reads extend beyond the contig end
throw new IllegalStateException("When calculating mismatches, we somehow don't have enough trailing reference context for read " + read.getReadName() + " at position " + ref.getLocus()); if ( refIndex >= refBases.length )
} break;
byte refChr = refBases[refIndex]; byte refChr = refBases[refIndex];
byte readChr = readBases[readIndex]; byte readChr = readBases[readIndex];