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

No reason to restrict HaplotypeScore to bi-allelic SNPs when the plumbing for multi-allelic events is already present.

This commit is contained in:
Eric Banks 2012-02-16 13:58:00 -05:00
parent 2f08846d82
commit 2f33c57060
1 changed files with 2 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -52,8 +52,7 @@ import java.util.*;
/**
* Consistency of the site with two (and only two) segregating haplotypes. Higher scores
* are indicative of regions with bad alignments, often leading to artifactual SNP and indel calls.
* Note that the Haplotype Score is only calculated for sites with read coverage; also, for SNPs, the
* site must be bi-allelic.
* Note that the Haplotype Score is only calculated for sites with read coverage.
*/
public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnotation {
private final static boolean DEBUG = false;
@ -65,12 +64,9 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
if (stratifiedContexts.size() == 0) // size 0 means that call was made by someone else and we have no data here
return null;
if (vc.isSNP() && !vc.isBiallelic())
return null;
final AlignmentContext context = AlignmentContextUtils.joinContexts(stratifiedContexts.values());
final int contextWingSize = Math.min(((int) ref.getWindow().size() - 1) / 2, MIN_CONTEXT_WING_SIZE);
final int contextWingSize = Math.min((ref.getWindow().size() - 1) / 2, MIN_CONTEXT_WING_SIZE);
final int contextSize = contextWingSize * 2 + 1;
final int locus = ref.getLocus().getStart() + (ref.getLocus().getStop() - ref.getLocus().getStart()) / 2;