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Updated for new version of samtools, which returns a sequence dictionary 

rather than a simple list of sequences.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@121 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-03-20 20:38:24 +00:00
parent 6e2d939905
commit b806a9cf68
1 changed files with 1 additions and 1 deletions
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2
playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java
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@ -250,7 +250,7 @@ public class IndelInspector extends CommandLineProgram {
setDefaultContigOrdering(); setDefaultContigOrdering();
return; return;
} }
List<SAMSequenceRecord> seqs = h.getSequences(); List<SAMSequenceRecord> seqs = h.getSequenceDictionary().getSequences();
if ( seqs == null ) { if ( seqs == null ) {
System.out.println("No reference sequence records found in SAM file header, " + System.out.println("No reference sequence records found in SAM file header, " +
"falling back to default contig ordering"); "falling back to default contig ordering");