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Corrected location and made more explicit the error message thrown if someone tries to read a VCF 3.3 file with indels, which is not supported. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3901 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-07-29 20:02:47 +00:00
parent 735ef19dc8
commit ba1a330293
1 changed files with 11 additions and 5 deletions
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16
java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
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@ -306,8 +306,16 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
Utils.warnUser("We are currently unable to parse out CNV encodings in VCF, we saw the following allele = " + allele);
return false;
}
else if ( ! Allele.acceptableAlleleBases(allele,isRef) ) {
throw new VCFParserException("Unparsable vcf record with allele " + allele);
else {
// check for VCF3.3 insertions or deletions
if (this.version != VCFHeaderVersion.VCF4_0) {
if ((allele.toUpperCase().charAt(0) == 'D') || (allele.toUpperCase().charAt(0) == 'D'))
throw new VCFParserException("Insertions/Deletions are not supported when reading 3.x VCF's. Please" +
" convert your file to VCF 4.0 using VCFTools, available at http://vcftools.sourceforge.net/index.html");
}
if ( ! Allele.acceptableAlleleBases(allele,isRef) )
throw new VCFParserException("Unparsable vcf record with allele " + allele);
}
return true;
}
@ -396,9 +404,7 @@ 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 ( !isSingleNucleotideEvent(alleles) ) {
if (this.version != VCFHeaderVersion.VCF4_0)
throw new VCFParserException("Saw Indel/non SNP event on a VCF 3.3 or earlier file. Please convert file to VCF4.0 with VCFTools before using the GATK on it");
locAndAlleles = clipAlleles(contig, pos, ref, alleles);
locAndAlleles = clipAlleles(contig, pos, ref, alleles);
} else {
locAndAlleles = new Pair<GenomeLoc, List<Allele>>(GenomeLocParser.createGenomeLoc(contig, pos), alleles);
}