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

@ -162,7 +162,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
// info fields
final int nAlleles = vc.getNAlleles();
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();
encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x00FF), BCF2Type.INT32);
@ -207,7 +207,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
}
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 ) {
if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
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(((LazyGenotypesContext)gc).getUnparsedGenotypeData().toString());
} else {
List<String> genotypeAttributeKeys = new ArrayList<String>();
if ( vc.hasGenotypes() ) {
genotypeAttributeKeys.addAll(calcVCFGenotypeKeys(vc));
}
List<String> genotypeAttributeKeys = calcVCFGenotypeKeys(vc, mHeader);
if ( ! genotypeAttributeKeys.isEmpty() ) {
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(genotypeFormatString);
@ -472,7 +469,7 @@ class VCFWriter extends IndexingVariantContextWriter {
* @param vc
* @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>();
boolean sawGoodGT = false;
@ -504,7 +501,7 @@ class VCFWriter extends IndexingVariantContextWriter {
sortedList = newList;
}
if ( sortedList.isEmpty() && vc.hasGenotypes() ) {
if ( sortedList.isEmpty() && header.hasGenotypingData() ) {
// this needs to be done in case all samples are no-calls
return Collections.singletonList(VCFConstants.GENOTYPE_KEY);
} else {