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Fixing the previous fix related to clipping. Adding extra reference padding in the HaplotypeCaller to get those larger alleles during GGA.

This commit is contained in:
Ryan Poplin 2012-06-04 12:49:36 -04:00
parent 320956ee4b
commit f11e7ebc3a
2 changed files with 4 additions and 4 deletions
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6
public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
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@ -58,9 +58,9 @@ public class ActiveRegion implements HasGenomeLocation, Comparable<ActiveRegion>
} }
public byte[] getActiveRegionReference( final IndexedFastaSequenceFile referenceReader, final int padding ) { public byte[] getActiveRegionReference( final IndexedFastaSequenceFile referenceReader, final int padding ) {
return referenceReader.getSubsequenceAt( activeRegionLoc.getContig(), return referenceReader.getSubsequenceAt( extendedLoc.getContig(),
Math.max(1, activeRegionLoc.getStart() - padding), Math.max(1, extendedLoc.getStart() - padding),
Math.min(referenceReader.getSequenceDictionary().getSequence(activeRegionLoc.getContig()).getSequenceLength(), activeRegionLoc.getStop() + padding) ).getBases(); Math.min(referenceReader.getSequenceDictionary().getSequence(extendedLoc.getContig()).getSequenceLength(), extendedLoc.getStop() + padding) ).getBases();
} }
public byte[] getFullReference( final IndexedFastaSequenceFile referenceReader ) { public byte[] getFullReference( final IndexedFastaSequenceFile referenceReader ) {

2
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -447,7 +447,7 @@ public class ReadUtils {
if (goalReached) { if (goalReached) {
// Is this base's reference position within this cigar element? Or did we use it all? // Is this base's reference position within this cigar element? Or did we use it all?
boolean endsWithinCigar = shift <= cigarElement.getLength(); boolean endsWithinCigar = shift < cigarElement.getLength();
// If it isn't, we need to check the next one. There should *ALWAYS* be a next one // If it isn't, we need to check the next one. There should *ALWAYS* be a next one
// since we checked if the goal coordinate is within the read length, so this is just a sanity check. // since we checked if the goal coordinate is within the read length, so this is just a sanity check.