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Renamed to more accurately describe its function. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2248 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-03 17:34:49 +00:00
parent c2017cc91b
commit df4e001a07
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java → java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
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@ -26,7 +26,7 @@ import java.util.List;
* Time: 12:38:17 PM
* To change this template use File | Settings | File Templates.
*/
public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
public class SnpCallRateByCoverageWalker extends LocusWalker<List<String>, String> {
// Control what goes into the variants file and what format that file should have
@Argument(fullName="lod_threshold", shortName="lod", doc="The lod threshold on which variants should be filtered", required=false) public Double LOD_THRESHOLD = 5.0;
@ -47,7 +47,7 @@ public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
}
public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
return (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 && context.getReads().size() != 0);
return (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 && context.getPileup().size() != 0);
}
public List<String> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {