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Better error message 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4273 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-09-14 05:04:26 +00:00
parent 248cc308b2
commit 71d2d69b41
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -734,7 +734,7 @@ public class GenomeAnalysisEngine {
Shard.ShardType shardType;
if(walker instanceof LocusWalker) {
if (readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.coordinate)
throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.coordinate, "Locus walkers can only walk over coordinate-sorted data. Please resort your input BAM file(s).");
throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.coordinate, "Locus walkers can only traverse coordinate-sorted data. Please resort your input BAM file(s) or set the Sort Order tag in the header appropriately.");
shardType = Shard.ShardType.LOCUS;
}
else if(walker instanceof ReadWalker || walker instanceof DuplicateWalker || walker instanceof ReadPairWalker)
@ -764,7 +764,7 @@ public class GenomeAnalysisEngine {
if (intervals != null && !intervals.isEmpty()) {
if(!readsDataSource.isEmpty() && readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.coordinate)
throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.coordinate, "Locus walkers can only walk over coordinate-sorted data. Please resort your input BAM file(s).");
throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.coordinate, "Locus walkers can only traverse coordinate-sorted data. Please resort your input BAM file(s) or set the Sort Order tag in the header appropriately.");
shardStrategy = ShardStrategyFactory.shatter(readsDataSource,
referenceDataSource.getReference(),