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Update error message so that it's clear ReadPair Walkers are exceptions

This commit is contained in:
Eric Banks 2011-11-15 09:22:57 -05:00
parent cde829899d
commit b66556f4a0
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -480,7 +480,7 @@ public class GenomeAnalysisEngine {
}
} else if (walker instanceof ReadPairWalker) {
if(readsDataSource != null && readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.queryname)
throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.queryname, "Read pair walkers can only walk over query name-sorted data. Please resort your input BAM file.");
throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.queryname, "Read pair walkers are exceptions in that they cannot be run on coordinate-sorted BAMs but instead require query name-sorted files. You will need to resort your input BAM file in query name order to use this walker.");
if(intervals != null && !intervals.isEmpty())
throw new UserException.CommandLineException("Pairs traversal cannot be used in conjunction with intervals.");