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

We were never clipping the VCF-provided ref base off the left end of the alleles for insertions, so the reference allele was never null (and downstream walkers would fail). Didn't this get tested with insertions at some point? 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3738 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-08 05:24:27 +00:00
parent 9a81f1d7ef
commit ada8c9931f
1 changed files with 13 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
View File

@ -387,11 +387,11 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
// find out our current location, and clip the alleles down to their minimum length
Pair<GenomeLoc, List<Allele>> locAndAlleles;
if (ref.length() > 1) {
attributes.put(ORIGINAL_ALLELE_LIST,alleles);
locAndAlleles = clipAlleles(contig, pos, ref, alleles);
if ( hasIndel(alleles) ) {
attributes.put(ORIGINAL_ALLELE_LIST,alleles);
locAndAlleles = clipAlleles(contig, pos, ref, alleles);
} else {
locAndAlleles = new Pair<GenomeLoc, List<Allele>>(GenomeLocParser.createGenomeLoc(contig, pos), alleles);
locAndAlleles = new Pair<GenomeLoc, List<Allele>>(GenomeLocParser.createGenomeLoc(contig, pos), alleles);
}
// a map to store our genotypes
@ -405,6 +405,15 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
return new VariantContext(name, locAndAlleles.first, locAndAlleles.second, genotypes, qual, filters, attributes);
}
private boolean hasIndel(List<Allele> alleles) {
int lengthOfFirstEntry = alleles.get(0).length();
for ( int i = 1; i < alleles.size(); i++ ) {
if ( alleles.get(i).length() != lengthOfFirstEntry )
return true;
}
return false;
}
class VCFParserException extends StingException {
public VCFParserException(String msg) {
super("Line " + lineNo + " generated parser exception " + msg);