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Handle the case where a walker is being run outside of the GATK framework, such as JUnit tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@222 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-03-29 01:50:27 +00:00
parent cb6a3b7e55
commit 7c6455fe36
1 changed files with 9 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
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@ -25,10 +25,16 @@ public abstract class Walker<MapType, ReduceType> {
protected PrintStream err = null; protected PrintStream err = null;
protected Walker() { protected Walker() {
if( GenomeAnalysisTK.Instance != null ) {
GenomeAnalysisTK.Instance.loadArgumentsIntoObject(this); GenomeAnalysisTK.Instance.loadArgumentsIntoObject(this);
out = GenomeAnalysisTK.Instance.out; out = GenomeAnalysisTK.Instance.out;
err = GenomeAnalysisTK.Instance.err; err = GenomeAnalysisTK.Instance.err;
} }
else {
out = System.out;
err = System.err;
}
}
/** /**
* Retrieve the toolkit, for peering into internal structures that can't * Retrieve the toolkit, for peering into internal structures that can't