Print coverage per reference base for each sample in a merged BAM file.

This  is a good example for how to untangle a merged BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@269 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java

@@ -0,0 +1,90 @@
+
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import net.sf.samtools.*;
+import org.broadinstitute.sting.gatk.*;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.refdata.rodGFF;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
+import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+import java.util.*;
+
+public class CoverageBySample extends LocusWalker<String, String> 
+{
+    List<String> sample_names = null;
+
+    public void initialize() 
+    { 
+        GenomeAnalysisTK toolkit = this.getToolkit();
+        SAMFileHeader header = toolkit.getSamReader().getFileHeader();
+        List<SAMReadGroupRecord> read_groups = header.getReadGroups();
+
+        sample_names    = new ArrayList<String>();
+
+        for (int i = 0; i < read_groups.size(); i++)
+        {
+            String sample_name = read_groups.get(i).getSample();
+            sample_names.add(sample_name);
+        } 
+    }
+
+    public String map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) 
+    {
+        String line = context.getLocation().getContig() + " " + context.getLocation().getStart() + " " ;
+        for (int i = 0; i < sample_names.size(); i++)
+        {
+            int count = countReadsBySample(context, sample_names.get(i));
+            line += " " + count;
+        }
+        line += "\n";
+        return line;
+    }
+
+    private int countReadsBySample(LocusContext context, String sample_name)
+    {
+        int count = 0;
+        for (int i = 0; i < context.getReads().size(); i++)
+        {
+            SAMRecord read = context.getReads().get(i);
+            Integer offset = context.getOffsets().get(i);
+            String RG = (String)(read.getAttribute("RG"));
+            String sample = read.getHeader().getReadGroup(RG).getSample();
+            if (sample == sample_name) 
+            { 
+                count += 1;
+            }
+        }
+        return count;
+    }
+
+    public void onTraversalDone() 
+    {
+        return;
+    }
+
+    public String reduceInit() 
+    { 
+        String header = "contig offset";
+        for (int i = 0; i < sample_names.size(); i++)
+        {
+            header += " " + sample_names.get(i);
+        }
+        header += "\n";
+        out.print(header);
+        return header;
+    }
+
+    public String reduce(String line, String sum) 
+    {
+        out.print(line);
+        return sum + line; 
+    }
+
+    
+}