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Fix for leniency actually working 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@47 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-03-13 16:26:18 +00:00
parent 10427f8191
commit 09307f768c
1 changed files with 2 additions and 1 deletions
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3
playground/java/src/org/broadinstitute/sting/atk/AnalysisTK.java
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@ -75,7 +75,6 @@ public class AnalysisTK extends CommandLineProgram {
} }
this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG, rods); this.engine = new TraversalEngine(INPUT_FILE, REF_FILE_ARG, rods);
engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true"));
//engine.testReference(); //engine.testReference();
ValidationStringency strictness; ValidationStringency strictness;
@ -97,6 +96,8 @@ public class AnalysisTK extends CommandLineProgram {
engine.setDebugging(! ( DEBUGGING_STR == null || DEBUGGING_STR.toLowerCase().equals("true"))); engine.setDebugging(! ( DEBUGGING_STR == null || DEBUGGING_STR.toLowerCase().equals("true")));
engine.setMaxReads(Integer.parseInt(MAX_READS_ARG)); engine.setMaxReads(Integer.parseInt(MAX_READS_ARG));
engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true"));
if ( REGION_STR != null ) { if ( REGION_STR != null ) {
engine.setLocation(REGION_STR); engine.setLocation(REGION_STR);
} }