From 6ae3f9e322772c939f7c494fe232adf465bd5f77 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sun, 14 Aug 2011 15:44:48 -0400
Subject: [PATCH] Wrapped clipping op information

The clipping op extra information being kept by this walker was specific to the walker, not to the read clipper. Created a wrapper ReadClipperWithData class that keeps the extra information and leaves the ReadClipper slim.

(this is a quick commit to unbreak the build, performing integration tests and will make further commits if necessary)
---
 .../sting/gatk/walkers/ClipReadsWalker.java   | 76 ++++++++++++-------
 1 file changed, 50 insertions(+), 26 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
index ca4e3f5e3..fc9c3a01e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
@@ -54,7 +54,7 @@ import java.util.regex.Pattern;
  * with poor quality scores, that match particular sequences, or that were generated by particular machine cycles.
  */
 @Requires({DataSource.READS})
-public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.ClippingData> {
+public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithData, ClipReadsWalker.ClippingData> {
     @Output
     PrintStream out;
 
@@ -99,6 +99,22 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
      */
     List<Pair<Integer, Integer>> cyclesToClip = null;
 
+    public class ReadClipperWithData extends ReadClipper {
+        private ClippingData data;
+
+        public ReadClipperWithData(SAMRecord read) {
+            super(read);
+        }
+
+        public ClippingData getData() {
+            return data;
+        }
+
+        public void setData(ClippingData data) {
+            this.data = data;
+        }
+    }
+
     /**
      * The initialize function.
      */
@@ -180,12 +196,12 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
      * @param read the read itself, as a SAMRecord
      * @return the ReadClipper object describing what should be done to clip this read
      */
-    public ReadClipper map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
+    public ReadClipperWithData map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
             if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES ) {
                 read = ReadUtils.replaceSoftClipsWithMatches(read);
             }
-            ReadClipper clipper = new ReadClipper(read);
+            ReadClipperWithData clipper = new ReadClipperWithData(read);
 
             //
             // run all three clipping modules
@@ -205,7 +221,7 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
      *
      * @param clipper
      */
-    private void clipSequences(ReadClipper clipper) {
+    private void clipSequences(ReadClipperWithData clipper) {
         if (sequencesToClip != null) {                // don't bother if we don't have any sequences to clip
             SAMRecord read = clipper.getRead();
 
@@ -223,8 +239,12 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
                     if (found) {
                         int start = match.start();
                         int stop = match.end() - 1;
-                        ClippingOp op = new ClippingOp(ClippingOp.ClippingType.MATCHES_CLIP_SEQ, start, stop, stc.seq);
+                        //ClippingOp op = new ClippingOp(ClippingOp.ClippingType.MATCHES_CLIP_SEQ, start, stop, stc.seq);
+                        ClippingOp op = new ClippingOp(start, stop);
                         clipper.addOp(op);
+                        ClippingData data = new ClippingData(sequencesToClip);
+                        data.incSeqClippedBases(stc.seq, op.getLength());
+                        clipper.setData(data);
                     }
                 }
             }
@@ -252,7 +272,7 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
      *
      * @param clipper
      */
-    private void clipCycles(ReadClipper clipper) {
+    private void clipCycles(ReadClipperWithData clipper) {
         if (cyclesToClip != null) {
             SAMRecord read = clipper.getRead();
 
@@ -270,8 +290,12 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
                     int start = startStop.first;
                     int stop = startStop.second;
 
-                    ClippingOp op = new ClippingOp(ClippingOp.ClippingType.WITHIN_CLIP_RANGE, start, stop, null);
+                    //ClippingOp op = new ClippingOp(ClippingOp.ClippingType.WITHIN_CLIP_RANGE, start, stop, null);
+                    ClippingOp op = new ClippingOp(start, stop);
                     clipper.addOp(op);
+                    ClippingData data = new ClippingData(sequencesToClip);
+                    data.incNRangeClippedBases(op.getLength());
+                    clipper.setData(data);
                 }
             }
         }
@@ -291,7 +315,7 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
      *
      * @param clipper
      */
-    private void clipBadQualityScores(ReadClipper clipper) {
+    private void clipBadQualityScores(ReadClipperWithData clipper) {
         SAMRecord read = clipper.getRead();
         int readLen = read.getReadBases().length;
         byte[] quals = read.getBaseQualities();
@@ -311,7 +335,12 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
         if (clipPoint != -1) {
             int start = read.getReadNegativeStrandFlag() ? 0 : clipPoint;
             int stop = read.getReadNegativeStrandFlag() ? clipPoint : readLen - 1;
-            clipper.addOp(new ClippingOp(ClippingOp.ClippingType.LOW_Q_SCORES, start, stop, null));
+            //clipper.addOp(new ClippingOp(ClippingOp.ClippingType.LOW_Q_SCORES, start, stop, null));
+            ClippingOp op = new ClippingOp(start, stop);
+            clipper.addOp(op);
+            ClippingData data = new ClippingData(sequencesToClip);
+            data.incNQClippedBases(op.getLength());
+            clipper.setData(data);
         }
     }
 
@@ -325,7 +354,7 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
         return new ClippingData(sequencesToClip);
     }
 
-    public ClippingData reduce(ReadClipper clipper, ClippingData data) {
+    public ClippingData reduce(ReadClipperWithData clipper, ClippingData data) {
         if ( clipper == null )
             return data;
 
@@ -340,23 +369,8 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
         data.nTotalBases += clipper.getRead().getReadLength();
         if (clipper.wasClipped()) {
             data.nClippedReads++;
-            for (ClippingOp op : clipper.getOps()) {
-                switch (op.type) {
-                    case LOW_Q_SCORES:
-                        data.incNQClippedBases(op.getLength());
-                        break;
-                    case WITHIN_CLIP_RANGE:
-                        data.incNRangeClippedBases(op.getLength());
-                        break;
-                    case MATCHES_CLIP_SEQ:
-                        data.incSeqClippedBases((String) op.extraInfo, op.getLength());
-                        break;
-                    default:
-                        throw new IllegalStateException("Unexpected Clipping operator type " + op);
-                }
-            }
         }
-
+        data.addData(clipper.getData());
         return data;
     }
 
@@ -417,6 +431,16 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
             seqClipCounts.put(seq, seqClipCounts.get(seq) + n);
         }
 
+        public void addData (ClippingData data) {
+            nTotalReads += data.nTotalReads;
+            nTotalBases += data.nTotalBases;
+            nClippedReads += data.nClippedReads;
+            nClippedBases += data.nClippedBases;
+            nQClippedBases += data.nQClippedBases;
+            nRangeClippedBases += data.nRangeClippedBases;
+            nSeqClippedBases += data.nSeqClippedBases;
+        }
+
         public String toString() {
             StringBuilder s = new StringBuilder();