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Reverting this change until we can figure out the right thing to do here.

This commit is contained in:
Ryan Poplin 2013-01-09 10:51:30 -05:00
parent c87ad8c0ef
commit 396bce1f28
1 changed files with 2 additions and 2 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -124,8 +124,8 @@ public class LikelihoodCalculationEngine {
final Haplotype haplotype = haplotypes.get(jjj); final Haplotype haplotype = haplotypes.get(jjj);
// TODO -- need to test against a reference/position with non-standard bases // TODO -- need to test against a reference/position with non-standard bases
if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) ) //if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) )
continue; // 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;