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Minimal support for reading in VCF4.1 files. Added TODOs that need to be fixed or cleaned up to truly support this version. VCF constants updated. Lower-case bases permitted. Please let's make sure to refactor once we're ready to support it for good. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5648 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-15 18:59:37 +00:00
parent 7e9051ea25
commit fe26954ac6
1 changed files with 6 additions and 6 deletions
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12
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -85,7 +85,7 @@ public class VariantContextAdaptors {
private static class DBSnpAdaptor extends VCAdaptor {
VariantContext convert(String name, Object input, ReferenceContext ref) {
DbSNPFeature dbsnp = (DbSNPFeature)input;
if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp),true) )
if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp)) )
return null;
Allele refAllele = Allele.create(DbSNPHelper.getReference(dbsnp), true);
@ -96,7 +96,7 @@ public class VariantContextAdaptors {
// add all of the alt alleles
for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
if ( ! Allele.acceptableAlleleBases(alt,false) ) {
if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp);
return null;
}
@ -148,7 +148,7 @@ public class VariantContextAdaptors {
*/
VariantContext convert(String name, Object input, ReferenceContext ref) {
GeliTextFeature geli = (GeliTextFeature)input;
if ( ! Allele.acceptableAlleleBases(String.valueOf(geli.getRefBase()),true) )
if ( ! Allele.acceptableAlleleBases(String.valueOf(geli.getRefBase())) )
return null;
Allele refAllele = Allele.create(String.valueOf(geli.getRefBase()), true);
@ -159,7 +159,7 @@ public class VariantContextAdaptors {
List<Allele> genotypeAlleles = new ArrayList<Allele>();
// add all of the alt alleles
for ( char alt : geli.getGenotype().toString().toCharArray() ) {
if ( ! Allele.acceptableAlleleBases(String.valueOf(alt),false) ) {
if ( ! Allele.acceptableAlleleBases(String.valueOf(alt)) ) {
return null;
}
Allele allele = Allele.create(String.valueOf(alt), false);
@ -306,7 +306,7 @@ public class VariantContextAdaptors {
throw new UnsupportedOperationException("Conversion from MAF to VariantContext requires a reference context, null received");
MafFeature maf = (MafFeature)input;
if ( ! Allele.acceptableAlleleBases(maf.getRefBases(),true) )
if ( ! Allele.acceptableAlleleBases(maf.getRefBases()) )
return null;
List<Allele> alleles = new ArrayList<Allele>();
@ -317,7 +317,7 @@ public class VariantContextAdaptors {
// add all of the alt alleles
for ( String alt : maf.getAllNonRefAlleleList() ) {
if ( ! Allele.acceptableAlleleBases(alt,false) ) {
if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp);
return null;
}