From ee5ab9536f54531e112f51bf69801fe0273a31cc Mon Sep 17 00:00:00 2001 From: depristo Date: Fri, 17 Apr 2009 03:11:59 +0000 Subject: [PATCH] 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 --- java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java | 1 - .../broadinstitute/sting/gatk/traversals/TraverseByReads.java | 3 ++- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 0d64c9e18..898852211 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -254,7 +254,6 @@ public class GenomeAnalysisTK extends CommandLineProgram { if ( REF_FILE_ARG == null ) Utils.scareUser(String.format("Locus-based traversals require a reference file but none was given")); - if ( INPUT_FILE == null ) { if ( walker.requiresReads() ) Utils.scareUser(String.format("Analysis %s requires reads, but none were given", Analysis_Name)); diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java index 11a9d7aed..9b33c789c 100644 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java @@ -63,7 +63,8 @@ public class TraverseByReads extends TraversalEngine { verifyingSamReadIter.setCheckOrderP(false); } - verifySortOrder(refFileName != null || walker.requiresOrderedReads()); + if ( samReader != null ) + verifySortOrder(refFileName != null || walker.requiresOrderedReads()); // Initialize the walker walker.initialize();