zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Changed the error for the record size mismatch in the genotyping engine to be a user error since it is possible 

to reach this state with input VCFs that contain the same event multiple times (and it's not something we want to
handle in the code).
This commit is contained in:
Eric Banks 2013-08-30 12:18:19 -04:00
parent 983097cff2
commit ea0deb1bb2
1 changed files with 3 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
View File

@ -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