zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Haplotype now consolidates cigars in setCigar 

-- This fixes edge base bugs where non-consolidated cigars are causing problems in users of the Haplotype object.  Input arguments are now checks (let's see if we blow up)
This commit is contained in:
Mark DePristo 2013-03-28 09:40:08 -04:00
parent 67cd407854
commit 8656bd5e29
1 changed files with 37 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

43
public/java/src/org/broadinstitute/sting/utils/haplotype/Haplotype.java
View File

@ -36,10 +36,12 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.Serializable;
import java.util.*;
import java.util.Arrays;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
public class Haplotype extends Allele {
private GenomeLoc genomeLocation = null;
@ -52,21 +54,36 @@ public class Haplotype extends Allele {
/**
* Main constructor
*
* @param bases bases
* @param isRef is reference allele?
* @param bases a non-null array of bases
* @param isRef is this the reference haplotype?
*/
public Haplotype( final byte[] bases, final boolean isRef ) {
super(bases.clone(), isRef);
}
/**
* Create a new non-ref haplotype
*
* @param bases a non-null array of bases
*/
public Haplotype( final byte[] bases ) {
this(bases, false);
}
/**
* Create a new haplotype with bases
*
* Requires bases.length == cigar.getReadLength()
*
* @param bases a non-null array of bases
* @param isRef is this the reference haplotype?
* @param alignmentStartHapwrtRef offset of this haplotype w.r.t. the reference
* @param cigar the cigar that maps this haplotype to the reference sequence
*/
public Haplotype( final byte[] bases, final boolean isRef, final int alignmentStartHapwrtRef, final Cigar cigar) {
this(bases, isRef);
this.alignmentStartHapwrtRef = alignmentStartHapwrtRef;
this.cigar = cigar;
setCigar(cigar);
}
/**
@ -127,6 +144,11 @@ public class Haplotype extends Allele {
this.alignmentStartHapwrtRef = alignmentStartHapwrtRef;
}
/**
* Get the cigar for this haplotype. Note that cigar is guarenteed to be consolidated
* in that multiple adjacent equal operates will have been merged
* @return the cigar of this haplotype
*/
public Cigar getCigar() {
return cigar;
}
@ -144,8 +166,17 @@ public class Haplotype extends Allele {
return AlignmentUtils.consolidateCigar(extendedHaplotypeCigar);
}
/**
* Set the cigar of this haplotype to cigar.
*
* Note that this function consolidates the cigar, so that 1M1M1I1M1M => 2M1I2M
*
* @param cigar a cigar whose readLength == length()
*/
public void setCigar( final Cigar cigar ) {
this.cigar = cigar;
this.cigar = AlignmentUtils.consolidateCigar(cigar);
if ( this.cigar.getReadLength() != length() )
throw new IllegalArgumentException("Read length " + length() + " not equal to the read length of the cigar " + cigar.getReadLength());
}
public boolean isArtificialHaplotype() {