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Merge pull request #388 from broadinstitute/eb_change_record_size_mismatch_to_user_error 

Changed the error for the record size mismatch in the genotyping engine ...
This commit is contained in:
Ryan Poplin 2013-08-30 10:29:54 -07:00
parent 5d79a6cbe0 ea0deb1bb2
commit add17dc463
1 changed files with 3 additions and 1 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -58,6 +58,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.DefaultHashMap;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.haplotype.EventMap;
import org.broadinstitute.sting.utils.haplotype.Haplotype;
@ -186,7 +187,8 @@ public class GenotypingEngine {
if( mergedVC == null ) { continue; }
if( eventsAtThisLoc.size() != mergedVC.getAlternateAlleles().size() ) {
throw new ReviewedStingException("Record size mismatch! Something went wrong in the merging of alleles.");
// this is possible in GGA mode when the same event is represented in multiple input records
throw new UserException("The same event (although possibly represented differently) is present in multiple input records at location " + loc + " and this is not something we can handle at this time. You will need to remove one of the records in order to proceed with your input file(s).");
}
final Map<VariantContext, Allele> mergeMap = new LinkedHashMap<>();
mergeMap.put(null, mergedVC.getReference()); // the reference event (null) --> the reference allele