From e26df45e8ebe98008fa8ba3f3296221c76e33900 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 18 Jun 2009 18:45:03 +0000
Subject: [PATCH] Different features can now be specified by repeatedly
 supplying the -F "featurename:arguments" option.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1043 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variants/IVFBinomialStrand.java  | 10 +++++++++-
 .../variants/IndependentVariantFeature.java       |  2 +-
 .../walkers/variants/VariantFiltrationWalker.java | 15 ++++++++-------
 3 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java
index 8a10ca335..3b00e2f09 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java
@@ -8,6 +8,14 @@ import net.sf.samtools.SAMRecord;
 import java.util.List;
 
 public class IVFBinomialStrand implements IndependentVariantFeature {
+    private double strandBalance = 0.5;
+
+    public IVFBinomialStrand(String arguments) {
+        if (arguments != null && !arguments.isEmpty()) {
+            strandBalance = Double.valueOf(arguments);
+        }
+    }
+
     public String getFeatureName() { return "binomial"; }
 
     public double[] compute(char ref, LocusContext context) {
@@ -35,7 +43,7 @@ public class IVFBinomialStrand implements IndependentVariantFeature {
                 }
             }
 
-            likelihoods[genotypeIndex] = Math.log10(MathUtils.binomialProbability(strandCounts[0], strandCounts[0] + strandCounts[1], 0.5));
+            likelihoods[genotypeIndex] = Math.log10(MathUtils.binomialProbability(strandCounts[0], strandCounts[0] + strandCounts[1], strandBalance));
         }
 
         return likelihoods;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java
index 7ccda69b3..84fd51088 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java
@@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
 
 public interface IndependentVariantFeature {
     public enum Genotype { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }
-
+    
     public String getFeatureName();
 
     public double[] compute(char ref, LocusContext context);
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
index a03673950..865593e47 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
@@ -18,15 +18,12 @@ import java.io.FileNotFoundException;
 
 @Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=rodVariants.class))
 public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
-    @Argument(fullName="features", shortName="F", doc="Comma-separated list of feature tests to apply to genotype posteriors.") public String FEATURES;
+    @Argument(fullName="features", shortName="F", doc="Feature test (optionally with arguments) to apply to genotype posteriors.  Syntax: 'testname:arg1,arg2,...,argN'") public String[] FEATURES;
     @Argument(fullName="variants_out", shortName="VO", doc="File to which modified variants should be written") public File VARIANTS_OUT;
 
-    private String[] features;
     private PrintWriter vwriter;
 
     public void initialize() {
-        features = FEATURES.split(",");
-
         try {
             vwriter = new PrintWriter(VARIANTS_OUT);
 
@@ -41,11 +38,15 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
     public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         rodVariants variant = (rodVariants) tracker.lookup("variant", null);
 
-        for (String feature : features) {
+        for (String feature : FEATURES) {
+            String[] featurePieces = feature.split(":");
+            String featureName = featurePieces[0];
+            String featureArgs = featurePieces[1];
+
             IndependentVariantFeature ivf;
             
-            if (feature.equalsIgnoreCase("binomial")) { ivf = new IVFBinomialStrand(); }
-            else { throw new StingException(String.format("Cannot understand feature '%s'\n", feature)); }
+            if (featureName.equalsIgnoreCase("binomialstrand")) { ivf = new IVFBinomialStrand(featureArgs); }
+            else { throw new StingException(String.format("Cannot understand feature '%s'", featureName)); }
 
             variant.adjustLikelihoods(ivf.compute(ref, context));
             vwriter.println(variant);