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Adding Unit test for Haplotype class. Used in HC's genotype given alleles mode.

This commit is contained in:
Ryan Poplin 2012-03-05 21:07:36 -05:00
parent b37461587d
commit 9b53250bef
1 changed files with 4 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
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@ -24,6 +24,7 @@
package org.broadinstitute.sting.utils; package org.broadinstitute.sting.utils;
import com.google.java.contract.Requires;
import net.sf.samtools.Cigar; 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;
@ -113,10 +114,11 @@ public class Haplotype {
return isReference; return isReference;
} }
public byte[] insertAllele( final Allele refAllele, final Allele altAllele, int refInsertLocation, final int hapStart, final Cigar haplotypeCigar ) { @Requires({"refInsertLocation >= 0", "hapStartInRefCoords >= 0"})
public byte[] insertAllele( final Allele refAllele, final Allele altAllele, int refInsertLocation, final int hapStartInRefCoords, final Cigar haplotypeCigar ) {
if( refAllele.length() != altAllele.length() ) { refInsertLocation++; } if( refAllele.length() != altAllele.length() ) { refInsertLocation++; }
int haplotypeInsertLocation = getHaplotypeCoordinateForReferenceCoordinate(hapStart, haplotypeCigar, refInsertLocation); int haplotypeInsertLocation = getHaplotypeCoordinateForReferenceCoordinate(hapStartInRefCoords, haplotypeCigar, refInsertLocation);
if( haplotypeInsertLocation == -1 ) { // desired change falls inside deletion so don't bother creating a new haplotype if( haplotypeInsertLocation == -1 ) { // desired change falls inside deletion so don't bother creating a new haplotype
return bases.clone(); return bases.clone();
} }