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Fixed bug in unsafe mode 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@78 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-17 15:28:04 +00:00
parent c74bd871b1
commit 0fd55d91d2
1 changed files with 2 additions and 1 deletions
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3
playground/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
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@ -526,7 +526,8 @@ public class TraversalEngine {
protected <M,R> int traverseByRead(ReadWalker<M,R> walker) { protected <M,R> int traverseByRead(ReadWalker<M,R> walker) {
if ( refFileName == null && ! walker.requiresOrderedReads() ) { if ( refFileName == null && ! walker.requiresOrderedReads() ) {
System.out.println("STATUS: No reference file provided and unordered reads are tolerated, enabling out of order read processing."); System.out.println("STATUS: No reference file provided and unordered reads are tolerated, enabling out of order read processing.");
verifyingSamReadIter.setCheckOrderP(false); if ( verifyingSamReadIter != null )
verifyingSamReadIter.setCheckOrderP(false);
} }
verifySortOrder( refFileName != null || walker.requiresOrderedReads()); verifySortOrder( refFileName != null || walker.requiresOrderedReads());