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Throw an error when genotype fields with mixed vector lengths are encountered

This commit is contained in:
Mark DePristo 2012-05-14 15:38:50 -04:00
parent afd2f1a3f9
commit 4968dcd36a
1 changed files with 7 additions and 2 deletions
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9
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
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@ -239,7 +239,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
}
private final int computeMaxSizeOfGenotypeFieldFromValues(final String field, final VariantContext vc) {
int size = 1;
int size = -1;
final GenotypesContext gc = vc.getGenotypes();
for ( final Genotype g : gc ) {
@ -248,8 +248,13 @@ class BCF2Writer extends IndexingVariantContextWriter {
if ( o instanceof List ) {
// only do compute if first value is of type list
final List values = (List)g.getAttribute(field);
if ( values != null )
if ( values != null ) {
if ( values.size() != size && size != -1 )
throw new ReviewedStingException("BUG: BCF2 codec doesn't currently support padding " +
"/ depadding of genotype fields with mixed length." +
"Occurred in field " + field + " at " + vc.getChr() + ":" + vc.getStart());
size = Math.max(size, values.size());
}
} else {
return 1;
}