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

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -85,7 +85,7 @@ public class VariantContextAdaptors {
private static class DBSnpAdaptor extends VCAdaptor { private static class DBSnpAdaptor extends VCAdaptor {
VariantContext convert(String name, Object input, ReferenceContext ref) { VariantContext convert(String name, Object input, ReferenceContext ref) {
DbSNPFeature dbsnp = (DbSNPFeature)input; DbSNPFeature dbsnp = (DbSNPFeature)input;
if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp),true) ) if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp)) )
return null; return null;
Allele refAllele = Allele.create(DbSNPHelper.getReference(dbsnp), true); Allele refAllele = Allele.create(DbSNPHelper.getReference(dbsnp), true);
@ -96,7 +96,7 @@ public class VariantContextAdaptors {
// add all of the alt alleles // add all of the alt alleles
for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) { for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
if ( ! Allele.acceptableAlleleBases(alt,false) ) { if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp); //System.out.printf("Excluding dbsnp record %s%n", dbsnp);
return null; return null;
} }
@ -148,7 +148,7 @@ public class VariantContextAdaptors {
*/ */
VariantContext convert(String name, Object input, ReferenceContext ref) { VariantContext convert(String name, Object input, ReferenceContext ref) {
GeliTextFeature geli = (GeliTextFeature)input; GeliTextFeature geli = (GeliTextFeature)input;
if ( ! Allele.acceptableAlleleBases(String.valueOf(geli.getRefBase()),true) ) if ( ! Allele.acceptableAlleleBases(String.valueOf(geli.getRefBase())) )
return null; return null;
Allele refAllele = Allele.create(String.valueOf(geli.getRefBase()), true); Allele refAllele = Allele.create(String.valueOf(geli.getRefBase()), true);
@ -159,7 +159,7 @@ public class VariantContextAdaptors {
List<Allele> genotypeAlleles = new ArrayList<Allele>(); List<Allele> genotypeAlleles = new ArrayList<Allele>();
// add all of the alt alleles // add all of the alt alleles
for ( char alt : geli.getGenotype().toString().toCharArray() ) { for ( char alt : geli.getGenotype().toString().toCharArray() ) {
if ( ! Allele.acceptableAlleleBases(String.valueOf(alt),false) ) { if ( ! Allele.acceptableAlleleBases(String.valueOf(alt)) ) {
return null; return null;
} }
Allele allele = Allele.create(String.valueOf(alt), false); 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"); throw new UnsupportedOperationException("Conversion from MAF to VariantContext requires a reference context, null received");
MafFeature maf = (MafFeature)input; MafFeature maf = (MafFeature)input;
if ( ! Allele.acceptableAlleleBases(maf.getRefBases(),true) ) if ( ! Allele.acceptableAlleleBases(maf.getRefBases()) )
return null; return null;
List<Allele> alleles = new ArrayList<Allele>(); List<Allele> alleles = new ArrayList<Allele>();
@ -317,7 +317,7 @@ public class VariantContextAdaptors {
// add all of the alt alleles // add all of the alt alleles
for ( String alt : maf.getAllNonRefAlleleList() ) { for ( String alt : maf.getAllNonRefAlleleList() ) {
if ( ! Allele.acceptableAlleleBases(alt,false) ) { if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp); //System.out.printf("Excluding dbsnp record %s%n", dbsnp);
return null; return null;
} }