From 71d2d69b41af4f1e4486b114dc535c44571de3a8 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 14 Sep 2010 05:04:26 +0000 Subject: [PATCH] Better error message git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4273 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 725bc3727..9ed27d046 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -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(),