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Fixed nasty bug in BCF2 writer for case where all genotypes are missing 

-- Previous code was looking for a -1 result from maxPloidy() but the result as actually 0, so instead of writing a diploid no call we were actually writing "unavailable" genotypes, and failing the BCF == VCF test in integration tests.  Fixed.
This commit is contained in:
Mark DePristo 2012-09-12 06:41:36 -04:00
parent 91f3204534
commit d1ba17df5d
2 changed files with 6 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
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@ -25,7 +25,6 @@
package org.broadinstitute.sting.utils.variantcontext; package org.broadinstitute.sting.utils.variantcontext;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import com.google.java.contract.Invariant;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import java.util.*; import java.util.*;
@ -413,6 +412,11 @@ public class GenotypesContext implements List<Genotype> {
return getGenotypes().get(i); return getGenotypes().get(i);
} }
/**
* What is the max ploidy among all samples? Returns 0 if no genotypes are present
*
* @return
*/
@Ensures("result >= 0") @Ensures("result >= 0")
public int getMaxPloidy() { public int getMaxPloidy() {
if ( maxPloidy == -1 ) { if ( maxPloidy == -1 ) {

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java
View File

@ -275,7 +275,7 @@ public abstract class BCF2FieldWriter {
nValuesPerGenotype = vc.getMaxPloidy(); nValuesPerGenotype = vc.getMaxPloidy();
// deal with the case where we have no call everywhere, in which case we write out diploid // deal with the case where we have no call everywhere, in which case we write out diploid
if ( nValuesPerGenotype == -1 ) if ( nValuesPerGenotype == 0 )
nValuesPerGenotype = 2; nValuesPerGenotype = 2;
super.start(encoder, vc); super.start(encoder, vc);