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Test for bad alleles so that we don't generate IndexOutOfBoundsExceptions

This commit is contained in:
Eric Banks 2011-07-07 23:01:03 -04:00
parent ce5a1c2cbe
commit 4cfe0dd857
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;
} else if ( !isSingleNucleotideEvent(alleles) ) {
ArrayList<Allele> newAlleles = new ArrayList<Allele>();
loc = clipAlleles(pos, ref, alleles, newAlleles);
loc = clipAlleles(pos, ref, alleles, newAlleles, lineNo);
alleles = newAlleles;
}
@ -504,7 +504,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
* @param clippedAlleles output list of clipped alleles
* @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
// 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)
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])
clipping = false;
}