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minor output changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1374 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-04 20:12:16 +00:00
parent 939b19e715
commit 3a8d923785
2 changed files with 4 additions and 3 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java
View File

@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.GenotypeUtils;
public class VECAlleleBalance implements VariantExclusionCriterion { //extends RatioFilter { public class VECAlleleBalance implements VariantExclusionCriterion { //extends RatioFilter {
//final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.TwoTailed; //final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.TwoTailed;
@ -62,7 +63,7 @@ public class VECAlleleBalance implements VariantExclusionCriterion { //extends
Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant); Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
int n = counts.first + counts.second; int n = counts.first + counts.second;
ratio = counts.first.doubleValue() / (double)n; ratio = counts.first.doubleValue() / (double)n;
exclude = (1.0 - ratio) < lowThreshold || ratio > highThreshold; exclude = GenotypeUtils.isHet(variant) && ((1.0 - ratio) < lowThreshold || ratio > highThreshold);
} }
public boolean useZeroQualityReads() { return false; } public boolean useZeroQualityReads() { return false; }

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
View File

@ -62,7 +62,7 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
if (LEARNING) { if (LEARNING) {
PrintWriter studyWriter = new PrintWriter(VARIANTS_OUT_HEAD + "." + STUDY_NAME); PrintWriter studyWriter = new PrintWriter(VARIANTS_OUT_HEAD + "." + STUDY_NAME);
swriters.put(STUDY_NAME, studyWriter); swriters.put(STUDY_NAME, studyWriter);
studyWriter.print("#Chr\tPosition\t"); studyWriter.print("Chr\tPosition\t");
} }
requestedFeatures = new ArrayList<IndependentVariantFeature>(); requestedFeatures = new ArrayList<IndependentVariantFeature>();
@ -257,7 +257,7 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
if (LEARNING) { if (LEARNING) {
rodDbSNP dbsnp = (rodDbSNP)tracker.lookup(knownSNPDBName, null); rodDbSNP dbsnp = (rodDbSNP)tracker.lookup(knownSNPDBName, null);
if ( dbsnp == null ) if ( dbsnp == null )
swriters.get(STUDY_NAME).print("no\tno\t"); swriters.get(STUDY_NAME).print("false\tfalse\t");
else else
swriters.get(STUDY_NAME).print(dbsnp.isSNP() + "\t" + dbsnp.isHapmap() + "\t"); swriters.get(STUDY_NAME).print(dbsnp.isSNP() + "\t" + dbsnp.isHapmap() + "\t");
swriters.get(STUDY_NAME).println(GenotypeUtils.isHet(variant)); swriters.get(STUDY_NAME).println(GenotypeUtils.isHet(variant));