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Protect against non-standard ref bases. Ryan, please review.

This commit is contained in:
Eric Banks 2012-12-26 15:46:21 -05:00
parent 75d5b88a3d
commit 275575462f
1 changed files with 5 additions and 0 deletions
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5
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -120,6 +120,11 @@ public class LikelihoodCalculationEngine {
for( int jjj = 0; jjj < numHaplotypes; jjj++ ) { for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
final Haplotype haplotype = haplotypes.get(jjj); final Haplotype haplotype = haplotypes.get(jjj);
// TODO -- need to test against a reference/position with non-standard bases
if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) )
continue;
final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) ); final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) );
previousHaplotypeSeen = haplotype; previousHaplotypeSeen = haplotype;