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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2011-07-07 23:01:24 -04:00
parent adb6fc910e 4cfe0dd857
commit cc143493e3
1 changed files with 4 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -225,7 +225,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
loc = pos + alleles.get(0).length() - 1; loc = pos + alleles.get(0).length() - 1;
} else if ( !isSingleNucleotideEvent(alleles) ) { } else if ( !isSingleNucleotideEvent(alleles) ) {
ArrayList<Allele> newAlleles = new ArrayList<Allele>(); ArrayList<Allele> newAlleles = new ArrayList<Allele>();
loc = clipAlleles(pos, ref, alleles, newAlleles); loc = clipAlleles(pos, ref, alleles, newAlleles, lineNo);
alleles = newAlleles; alleles = newAlleles;
} }
@ -504,7 +504,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
* @param clippedAlleles output list of clipped alleles * @param clippedAlleles output list of clipped alleles
* @return a list of alleles, clipped to the reference * @return a list of alleles, clipped to the reference
*/ */
protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles) { protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles, int lineNo) {
// Note that the computation of forward clipping here is meant only to see whether there is a common // Note that the computation of forward clipping here is meant only to see whether there is a common
// base to all alleles, and to correctly compute reverse clipping, // base to all alleles, and to correctly compute reverse clipping,
@ -522,6 +522,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
} }
if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0) if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0)
clipping = false; clipping = false;
else if (ref.length() == reverseClipped)
generateException("bad alleles encountered", lineNo);
else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1]) else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1])
clipping = false; clipping = false;
} }