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Better window size error message 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4290 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-09-15 20:40:56 +00:00
parent b5d2e299d2
commit fb6d7d19f9
1 changed files with 2 additions and 3 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -425,11 +425,10 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
// let's double check now that the read fits after the shift // let's double check now that the read fits after the shift
if ( read.getAlignmentEnd() > normal_context.getStop()) { if ( read.getAlignmentEnd() > normal_context.getStop()) {
// ooops, looks like the read does not fit into the window even after the latter was shifted!! // ooops, looks like the read does not fit into the window even after the latter was shifted!!
throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.coordinate, read, "Read "+read.getReadName()+": out of coverage window bounds. Probably window is too small.\n"+ throw new UserException.BadArgumentValue("window_size", "Read "+read.getReadName()+": out of coverage window bounds. Probably window is too small, so increase the value of the window_size argument.\n"+
"Read length="+read.getReadLength()+"; cigar="+read.getCigarString()+"; start="+ "Read length="+read.getReadLength()+"; cigar="+read.getCigarString()+"; start="+
read.getAlignmentStart()+"; end="+read.getAlignmentEnd()+ read.getAlignmentStart()+"; end="+read.getAlignmentEnd()+
"; window start (after trying to accomodate the read)="+normal_context.getStart()+ "; window start (after trying to accomodate the read)="+normal_context.getStart()+"; window end="+normal_context.getStop());
"; window end="+normal_context.getStop());
} }
} }