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Filters should only be applied to the new VC if the old VC had filters applied

This commit is contained in:
Menachem Fromer 2011-07-13 11:58:16 -04:00
parent 73735863b0
commit fa3ff53508
1 changed files with 4 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -220,6 +220,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
}
else {
unprocessedList.add(vc); // Finished with the unprocessed variant, and writer can enforce sorting on-the-fly
if (DEBUG)
logger.debug("Unprocessed variant = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
}
int numReads = 0;
@ -1105,7 +1108,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
this.alleles = vc.getAlleles();
this.genotypes = new HashMap<String, Genotype>(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
this.negLog10PError = vc.getNegLog10PError();
this.filters = vc.getFilters();
this.filters = vc.filtersWereApplied() ? vc.getFilters() : null;
this.attributes = new HashMap<String, Object>(vc.getAttributes());
}