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Adding genotype given alleles mode to the HaplotypeCaller.

This commit is contained in:
Ryan Poplin 2012-05-30 15:07:01 -04:00
parent f987d5487e
commit 5dd811f84a
2 changed files with 5 additions and 5 deletions
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8
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
View File

@ -158,12 +158,12 @@ public class Haplotype {
} }
@Requires({"refInsertLocation >= 0"}) @Requires({"refInsertLocation >= 0"})
public byte[] insertAllele( final Allele refAllele, final Allele altAllele, int refInsertLocation ) { public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, int refInsertLocation ) {
if( refAllele.length() != altAllele.length() ) { refInsertLocation++; } if( refAllele.length() != altAllele.length() ) { refInsertLocation++; }
int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(alignmentStartHapwrtRef, cigar, refInsertLocation, ReadUtils.ClippingTail.RIGHT_TAIL, true); int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(alignmentStartHapwrtRef, cigar, refInsertLocation, ReadUtils.ClippingTail.RIGHT_TAIL, true);
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 new Haplotype(bases.clone());
} }
byte[] newHaplotype; byte[] newHaplotype;
@ -196,10 +196,10 @@ public class Haplotype {
} }
} }
} catch (Exception e) { // event already on haplotype is too large/complex to insert another allele, most likely because of not enough reference padding } catch (Exception e) { // event already on haplotype is too large/complex to insert another allele, most likely because of not enough reference padding
return bases.clone(); return new Haplotype(bases.clone());
} }
return newHaplotype; return new Haplotype(newHaplotype);
} }
public static LinkedHashMap<Allele,Haplotype> makeHaplotypeListFromAlleles(List<Allele> alleleList, int startPos, ReferenceContext ref, public static LinkedHashMap<Allele,Haplotype> makeHaplotypeListFromAlleles(List<Allele> alleleList, int startPos, ReferenceContext ref,

2
public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
View File

@ -154,7 +154,7 @@ public class HaplotypeUnitTest extends BaseTest {
final Allele h1altAllele = Allele.create(alt, false); final Allele h1altAllele = Allele.create(alt, false);
h.setAlignmentStartHapwrtRef(0); h.setAlignmentStartHapwrtRef(0);
h.setCigar(cigar); h.setCigar(cigar);
final Haplotype h1 = new Haplotype( h.insertAllele(h1refAllele, h1altAllele, loc - INDEL_PADDING_BASE) ); final Haplotype h1 = h.insertAllele(h1refAllele, h1altAllele, loc - INDEL_PADDING_BASE);
final Haplotype h1expected = new Haplotype(newHap.getBytes()); final Haplotype h1expected = new Haplotype(newHap.getBytes());
Assert.assertEquals(h1, h1expected); Assert.assertEquals(h1, h1expected);
} }