From c556a97f175340b5b290762e21c1406c6ba4f783 Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Apr 2009 02:34:03 +0000
Subject: [PATCH] Skeleton of Somatic Coverage tool

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@342 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/SomaticCoverageWalker.java   | 115 ++++++++++++++++++
 1 file changed, 115 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
new file mode 100644
index 000000000..2536fab2a
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
@@ -0,0 +1,115 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import net.sf.samtools.SAMRecord;
+
+import java.util.List;
+import java.util.Formatter;
+import static java.lang.Math.log10;
+
+import edu.mit.broad.picard.genotype.DiploidGenotype;
+import edu.mit.broad.picard.PicardException;
+
+public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
+
+    @Argument(fullName = "tumor_sample_name", shortName = "1", required = true)
+    String tumorSampleName = "TCGA-06-0188-01A-01W";  // FIXME: cmdline parsing not working!
+
+    @Argument(fullName = "normal_sample_name", shortName = "2", required = true)
+    String normalSampleName = "TCGA-06-0188-10B-01W"; // FIXME: cmdline parsing not working!
+
+    public void initialize() {
+    }
+
+    public String walkerType() { return "ByLocus"; }
+
+    // Do we actually want to operate on the context?
+    public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
+        return true;    // We are keeping all the reads
+    }
+
+
+
+    // Map over the org.broadinstitute.sting.gatk.LocusContext
+    int MAPPING_QUALITY_THRESHOLD = 1;
+    int totalSites;
+    int tumorCovered;
+    int normalCovered;
+    int somaticCovered;
+
+    public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
+
+        List<SAMRecord> reads = context.getReads();
+        int tumorDepth = 0;
+        int normalDepth = 0;
+        for ( int i = 0; i < reads.size(); i++ )
+        {
+            SAMRecord read = reads.get(i);
+
+            // TODO: could this be done better elsewhere?
+            // only process primary, non duplicate alignments
+            // that come from fully mapped pairs with a mappign quality threshold >= x
+            if (read.getNotPrimaryAlignmentFlag() ||
+                read.getDuplicateReadFlag() ||
+                read.getReadUnmappedFlag()
+        ||
+                read.getMateUnmappedFlag() ||
+                read.getMappingQuality() < MAPPING_QUALITY_THRESHOLD
+                    ) {
+                continue;
+            }
+
+            String rg = (String) read.getAttribute("RG");
+            String sample = read.getHeader().getReadGroup(rg).getSample();
+
+
+
+            if (normalSampleName.equals(sample)) {
+                normalDepth++;
+            } else if (tumorSampleName.equals(sample)) {
+                tumorDepth++;
+            } else {
+                throw new RuntimeException("Unknown Sample Name: " + sample);
+            }
+
+        }
+
+
+        boolean isTumorCovered = tumorDepth >= 14;
+        boolean isNormalCovered = normalDepth >= 8;
+
+        if (isTumorCovered) { tumorCovered++; }
+        if (isNormalCovered) { normalCovered++; }
+        if (isTumorCovered && isNormalCovered) {somaticCovered++; }
+        totalSites++;
+
+        if (totalSites % 20000 == 0) {
+            out.println(String.format("%s:%d %d %d %d %d", context.getContig(), context.getPosition(), totalSites, tumorCovered, normalCovered, somaticCovered));
+        }
+
+        return 1;
+    }
+
+    // Given result of map function
+    public Integer reduceInit() {
+        return 0;
+    }
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+
+    @Override
+    public void onTraversalDone(Integer result) {
+        out.println(String.format("FINAL - %d %d %d %d", totalSites, tumorCovered, normalCovered, somaticCovered));
+    }
+
+
+
+}
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