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trivial checking / flagging issues to enable testing of merging iterator performance 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@460 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-17 03:11:59 +00:00
parent dbf2344cef
commit ee5ab9536f
2 changed files with 2 additions and 2 deletions
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1
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -254,7 +254,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
if ( REF_FILE_ARG == null ) if ( REF_FILE_ARG == null )
Utils.scareUser(String.format("Locus-based traversals require a reference file but none was given")); Utils.scareUser(String.format("Locus-based traversals require a reference file but none was given"));
if ( INPUT_FILE == null ) { if ( INPUT_FILE == null ) {
if ( walker.requiresReads() ) if ( walker.requiresReads() )
Utils.scareUser(String.format("Analysis %s requires reads, but none were given", Analysis_Name)); Utils.scareUser(String.format("Analysis %s requires reads, but none were given", Analysis_Name));

3
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
View File

@ -63,7 +63,8 @@ public class TraverseByReads extends TraversalEngine {
verifyingSamReadIter.setCheckOrderP(false); verifyingSamReadIter.setCheckOrderP(false);
} }
verifySortOrder(refFileName != null || walker.requiresOrderedReads()); if ( samReader != null )
verifySortOrder(refFileName != null || walker.requiresOrderedReads());
// Initialize the walker // Initialize the walker
walker.initialize(); walker.initialize();