dumps out base qualities per position for use in making boxplots

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@119 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,54 @@
+package org.broadinstitute.sting.gatk.walkers;
+
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.utils.Utils;
+import edu.mit.broad.picard.reference.ReferenceSequence;
+
+import java.util.Iterator;
+import java.util.List;
+import static java.lang.reflect.Array.*;
+
+public class BaseQualityDumpWalker extends BasicReadWalker<Integer, Integer> {
+
+    protected final int MIN_TARGET_EDIT_DISTANCE = 0; //5;
+    protected final int MAX_TARGET_EDIT_DISTANCE = 4; //10;
+
+    public String getName() {
+        return "Base_Quality_Dump";
+    }
+
+    // Do we actually want to operate on the context?
+    public boolean filter(LocusContext context, SAMRecord read) {
+	    // we only want aligned reads
+	    return !read.getReadUnmappedFlag();
+    }
+
+    public Integer map(LocusContext context, SAMRecord read) {
+
+        int editDist = Integer.parseInt(read.getAttribute("NM").toString());
+
+        // ignore alignments with indels for now
+        if ( read.getAlignmentBlocks().size() == 1 &&
+             editDist >= MIN_TARGET_EDIT_DISTANCE &&
+             editDist <= MAX_TARGET_EDIT_DISTANCE ) {
+
+            String qualStr = read.getBaseQualityString();
+            int[] scores = new int[qualStr.length()];
+            boolean reverseFlag = read.getReadNegativeStrandFlag();
+            for ( int i = 0; i < qualStr.length(); i++)
+                scores[(reverseFlag ? (qualStr.length()-1-i) : i)] += (int)qualStr.charAt(i) - 33;
+            for ( int i = 0; i < scores.length; i++ )
+                System.out.print(scores[i] + " ");
+            System.out.println("");
+        }
+
+        return 1;
+    }
+
+    public Integer reduceInit() { return 0; }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+}