OverlapWithBedInIntervalWalker calculates the average per-input-interval coverage by the BED intervals track

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5468 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/GCcontentIntervalWalker.java

@@ -40,7 +40,7 @@ import java.io.PrintStream;
 import java.util.*;
 
 /**
- * Walks along reference and calculates the GC content for each interval defined in "intervals" ROD.
+ * Walks along reference and calculates the GC content for each interval.
  */
 @Allows(value = {DataSource.REFERENCE})
 @Requires(value = {DataSource.REFERENCE})

java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/GeneNamesIntervalWalker.java

@@ -42,7 +42,7 @@ import java.util.List;
 import java.util.Set;
 
 /**
- * Walks along reference and calculates the genes (from "refseq" ROD) for each interval defined in "intervals" ROD.
+ * Walks along reference and calculates the genes (from "refseq" ROD) for each interval.
  */
 @Allows(value = {DataSource.REFERENCE})
 @Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = GeneNamesIntervalWalker.REFSEQ_ROD_NAME, type = AnnotatorInputTableFeature.class)})
@@ -138,5 +138,4 @@ class GeneNames {
 
         return sb.toString();
     }
-}
-
+}

java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/OverlapWithBedInIntervalWalker.java

@@ -0,0 +1,129 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.oneoffprojects.walkers.CNV;
+
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.collections.Pair;
+
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * Walks along reference and calculates the percent overlap with the BED file intervals for each -L interval.
+ */
+@Allows(value = {DataSource.REFERENCE})
+@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = OverlapWithBedInIntervalWalker.INTERVALS_ROD_NAME, type = ReferenceOrderedDatum.class)})
+
+public class OverlapWithBedInIntervalWalker extends RodWalker<CumulativeBaseOverlapCount, CumulativeBaseOverlapCount> {
+    @Output
+    protected PrintStream out;
+
+    public final static String INTERVALS_ROD_NAME = "intervals";
+
+
+    public boolean isReduceByInterval() {
+        return true;
+    }
+
+    public void initialize() {
+    }
+
+    public boolean generateExtendedEvents() {
+        return false;
+    }
+
+    public CumulativeBaseOverlapCount reduceInit() {
+        return new CumulativeBaseOverlapCount();
+    }
+
+    /**
+     * @param tracker the meta-data tracker
+     * @param ref     the reference base
+     * @param context the context for the given locus
+     * @return statistics of and list of all phased VariantContexts and their base pileup that have gone out of cacheWindow range.
+     */
+    public CumulativeBaseOverlapCount map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if (tracker == null)
+            return null;
+
+        return new CumulativeBaseOverlapCount().addIntervals(tracker.getGATKFeatureMetaData(INTERVALS_ROD_NAME, true));
+    }
+
+    public CumulativeBaseOverlapCount reduce(CumulativeBaseOverlapCount add, CumulativeBaseOverlapCount runningCount) {
+        if (add == null)
+            add = new CumulativeBaseOverlapCount();
+
+        return runningCount.addIn(add);
+    }
+
+    /**
+     * @param results the genes found in each interval.
+     */
+    public void onTraversalDone(List<Pair<GenomeLoc, CumulativeBaseOverlapCount>> results) {
+        for (Pair<GenomeLoc, CumulativeBaseOverlapCount> result : results ) {
+            GenomeLoc loc = result.getFirst();
+
+            CumulativeBaseOverlapCount overlapCount = result.getSecond();
+            double meanOverlap = ((double) overlapCount.totalOverlapCount) / loc.size();
+
+            out.println(loc + "\t" + meanOverlap);
+        }
+    }
+}
+
+class CumulativeBaseOverlapCount {
+    public int totalOverlapCount;
+
+    public CumulativeBaseOverlapCount() {
+        this.totalOverlapCount = 0;
+    }
+
+    public CumulativeBaseOverlapCount addIn(CumulativeBaseOverlapCount other) {
+        this.totalOverlapCount += other.totalOverlapCount;
+
+        return this;
+    }
+
+    public CumulativeBaseOverlapCount addIntervals(List<GATKFeature> interval) {
+        totalOverlapCount += interval.size();
+
+        return this;
+    }
+
+    public String toString() {
+        StringBuilder sb = new StringBuilder();
+
+        sb.append(totalOverlapCount);
+
+        return sb.toString();
+    }
+}