From 80b531f6951874eae187b8d2b10c0da3ad60b85a Mon Sep 17 00:00:00 2001
From: Ami Levy-Moonshine <ami@broadinstitute.org>
Date: Fri, 4 Jan 2013 14:27:50 -0500
Subject: [PATCH] emit all sites where more than 90% of the samples have good
 coverage

---
 .../coverage/CoveredByNSamplesSites.java      | 94 +++++++++++++++++++
 1 file changed, 94 insertions(+)
 create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoveredByNSamplesSites.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoveredByNSamplesSites.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoveredByNSamplesSites.java
new file mode 100644
index 000000000..ea31a58f1
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoveredByNSamplesSites.java
@@ -0,0 +1,94 @@
+package org.broadinstitute.sting.gatk.walkers.coverage;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: ami
+ * Date: 1/3/13
+ * Time: 1:51 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.Map;
+
+@By(DataSource.REFERENCE_ORDERED_DATA)
+public class CoveredByNSamplesSites extends RodWalker<Integer,Integer> implements TreeReducible<Integer> {
+    @Output
+    PrintStream out;
+
+    @Output(fullName = "OutputIntervals", shortName = "intervals", doc = "Name of file for output intervals", required = true)
+    File intervalFile;
+
+    @ArgumentCollection
+    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
+
+
+    @Argument(fullName = "minCoverage", shortName = "minCov",doc = "only samples that have coverage higher then the min are taking into account", required =  false)
+    int minCoverage = 10;
+
+    @Argument(fullName = "samplePercentage", shortName = "percentage",doc = "only sites that have more than samplePercentage samples with minCoverage", required = false)
+    double samplePercentage = 0.9;
+
+    @Override
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context){
+        if(tracker == null)
+            return 0;
+
+        Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
+        if (vcs.size() == 0)
+            return 0;
+
+        for (VariantContext vc : vcs){
+            int countCoveredSamples = 0;
+            final GenotypesContext genotypes =  vc.getGenotypes();
+            final int numOfGenotype = genotypes.size();
+            for (Genotype g : genotypes){
+                if (g.getDP() > minCoverage)
+                    countCoveredSamples++;
+            }
+            if (countCoveredSamples/numOfGenotype >= samplePercentage)
+                out.print(ref.getLocus());
+
+        }
+
+        return 1;
+    }
+
+    @Override
+    public Integer reduceInit() { return 0; }
+
+    @Override
+    public Integer reduce(Integer value, Integer sum) { return value + sum; }
+
+    @Override
+    public Integer treeReduce(Integer lhs, Integer rhs) {
+        return lhs + rhs;
+    }
+
+    /**
+     * Tell the user the number of loci processed and close out the new variants file.
+     *
+     * @param result  the number of loci seen.
+     */
+    public void onTraversalDone(Integer result) {
+        logger.info("Processed " + result + " loci.\n");
+    }
+}