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

Bugfix for VCFWriter in the case where there are no genotypes in the VC but genotypes in the header

This commit is contained in:
Mark DePristo 2012-05-21 16:24:23 -04:00
parent 4846bf5c8e
commit 4bde24f020
2 changed files with 7 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
View File

@ -162,7 +162,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
// info fields // info fields
final int nAlleles = vc.getNAlleles(); final int nAlleles = vc.getNAlleles();
final int nInfo = vc.getAttributes().size(); final int nInfo = vc.getAttributes().size();
final int nGenotypeFormatFields = VCFWriter.calcVCFGenotypeKeys(vc).size(); final int nGenotypeFormatFields = VCFWriter.calcVCFGenotypeKeys(vc, header).size();
final int nSamples = vc.getNSamples(); final int nSamples = vc.getNSamples();
encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x00FF), BCF2Type.INT32); encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x00FF), BCF2Type.INT32);
@ -207,7 +207,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
} }
private byte[] buildSamplesData(final VariantContext vc) throws IOException { private byte[] buildSamplesData(final VariantContext vc) throws IOException {
List<String> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc); List<String> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc, header);
for ( final String field : genotypeFields ) { for ( final String field : genotypeFields ) {
if ( field.equals(VCFConstants.GENOTYPE_KEY) ) { if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
addGenotypes(vc); addGenotypes(vc);

13
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
View File

@ -254,13 +254,10 @@ class VCFWriter extends IndexingVariantContextWriter {
mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write(VCFConstants.FIELD_SEPARATOR);
mWriter.write(((LazyGenotypesContext)gc).getUnparsedGenotypeData().toString()); mWriter.write(((LazyGenotypesContext)gc).getUnparsedGenotypeData().toString());
} else { } else {
List<String> genotypeAttributeKeys = new ArrayList<String>(); List<String> genotypeAttributeKeys = calcVCFGenotypeKeys(vc, mHeader);
if ( vc.hasGenotypes() ) { if ( ! genotypeAttributeKeys.isEmpty() ) {
genotypeAttributeKeys.addAll(calcVCFGenotypeKeys(vc)); final String genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
}
if ( genotypeAttributeKeys.size() > 0 ) {
String genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write(VCFConstants.FIELD_SEPARATOR);
mWriter.write(genotypeFormatString); mWriter.write(genotypeFormatString);
@ -472,7 +469,7 @@ class VCFWriter extends IndexingVariantContextWriter {
* @param vc * @param vc
* @return an ordered list of genotype fields in use in VC. If vc has genotypes this will always include GT first * @return an ordered list of genotype fields in use in VC. If vc has genotypes this will always include GT first
*/ */
public static List<String> calcVCFGenotypeKeys(VariantContext vc) { public static List<String> calcVCFGenotypeKeys(final VariantContext vc, final VCFHeader header) {
Set<String> keys = new HashSet<String>(); Set<String> keys = new HashSet<String>();
boolean sawGoodGT = false; boolean sawGoodGT = false;
@ -504,7 +501,7 @@ class VCFWriter extends IndexingVariantContextWriter {
sortedList = newList; sortedList = newList;
} }
if ( sortedList.isEmpty() && vc.hasGenotypes() ) { if ( sortedList.isEmpty() && header.hasGenotypingData() ) {
// this needs to be done in case all samples are no-calls // this needs to be done in case all samples are no-calls
return Collections.singletonList(VCFConstants.GENOTYPE_KEY); return Collections.singletonList(VCFConstants.GENOTYPE_KEY);
} else { } else {