zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Adding AF bin stratification for VariantEval. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5728 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-03 15:22:50 +00:00
parent 870e65a685
commit 70f8ab6f89
1 changed files with 41 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

41
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java 100755
View File

@ -0,0 +1,41 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
import org.broadinstitute.sting.utils.MathUtils;
import java.util.ArrayList;
import java.util.Set;
public class AlleleFrequency extends VariantStratifier {
// needs to know the variant context
private ArrayList<String> states;
@Override
public void initialize(Set<SortableJexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames, Set<String> contigNames) {
states = new ArrayList<String>();
for( double a = 0.000; a <= 1.005; a += 0.005 ) {
states.add(String.format("%.3f", a));
}
}
public ArrayList<String> getAllStates() {
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
if (eval != null) {
try {
relevantStates.add(String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF") / 5.0, 3))));
} catch (Exception e) {
return relevantStates;
}
}
return relevantStates;
}
}