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Bug fix in HaplotypeCaller's GENOTYPE_GIVEN_ALLELES mode for insertions greater than length 1. The allele being genotyped was off by one base pair.

This commit is contained in:
Ryan Poplin 2012-02-22 19:00:04 -05:00
parent ca7b5e068f
commit 8695738400
1 changed files with 1 additions and 3 deletions
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4
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
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@ -28,9 +28,7 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement; import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator; import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
import java.util.Arrays; import java.util.Arrays;
@ -133,7 +131,7 @@ public class Haplotype {
} }
} else if( refAllele.length() < altAllele.length() ) { // insertion } else if( refAllele.length() < altAllele.length() ) { // insertion
final int altAlleleLength = altAllele.length(); final int altAlleleLength = altAllele.length();
for( int iii = newHaplotype.length -1; iii > haplotypeInsertLocation + altAlleleLength; iii-- ) { for( int iii = newHaplotype.length - 1; iii > haplotypeInsertLocation + altAlleleLength - 1; iii-- ) {
newHaplotype[iii] = newHaplotype[iii-altAlleleLength]; newHaplotype[iii] = newHaplotype[iii-altAlleleLength];
} }
for( int iii = 0; iii < altAlleleLength; iii++ ) { for( int iii = 0; iii < altAlleleLength; iii++ ) {