From 09307f768cb5d2ce6743d28962affc093e46f977 Mon Sep 17 00:00:00 2001 From: depristo Date: Fri, 13 Mar 2009 16:26:18 +0000 Subject: [PATCH] Fix for leniency actually working git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@47 348d0f76-0448-11de-a6fe-93d51630548a --- .../java/src/org/broadinstitute/sting/atk/AnalysisTK.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java b/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java index bb9e0e3c1..86ac6ba49 100644 --- a/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java +++ b/playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java @@ -75,7 +75,6 @@ public class AnalysisTK extends CommandLineProgram { } this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG, rods); - engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true")); //engine.testReference(); ValidationStringency strictness; @@ -97,6 +96,8 @@ public class AnalysisTK extends CommandLineProgram { engine.setDebugging(! ( DEBUGGING_STR == null || DEBUGGING_STR.toLowerCase().equals("true"))); engine.setMaxReads(Integer.parseInt(MAX_READS_ARG)); + engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true")); + if ( REGION_STR != null ) { engine.setLocation(REGION_STR); }