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Fixed integration tests

This commit is contained in:
Mauricio Carneiro 2011-08-14 16:38:20 -04:00
parent 6ae3f9e322
commit c7b69a4574
1 changed files with 39 additions and 24 deletions
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63
public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
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@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation;
import org.broadinstitute.sting.utils.clipreads.ReadClipper;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.yaml.snakeyaml.events.SequenceStartEvent;
import java.io.File;
import java.io.PrintStream;
@ -99,22 +100,6 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
*/
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.
*/
@ -201,7 +186,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES ) {
read = ReadUtils.replaceSoftClipsWithMatches(read);
}
ReadClipperWithData clipper = new ReadClipperWithData(read);
ReadClipperWithData clipper = new ReadClipperWithData(read, sequencesToClip);
//
// run all three clipping modules
@ -224,6 +209,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
private void clipSequences(ReadClipperWithData clipper) {
if (sequencesToClip != null) { // don't bother if we don't have any sequences to clip
SAMRecord read = clipper.getRead();
ClippingData data = clipper.getData();
for (SeqToClip stc : sequencesToClip) {
// we have a pattern for both the forward and the reverse strands
@ -242,12 +228,11 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
//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);
}
}
}
clipper.setData(data);
}
}
@ -275,6 +260,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
private void clipCycles(ReadClipperWithData clipper) {
if (cyclesToClip != null) {
SAMRecord read = clipper.getRead();
ClippingData data = clipper.getData();
for (Pair<Integer, Integer> p : cyclesToClip) { // iterate over each cycle range
int cycleStart = p.first;
@ -293,11 +279,10 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
//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);
}
}
clipper.setData(data);
}
}
@ -317,6 +302,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
*/
private void clipBadQualityScores(ReadClipperWithData clipper) {
SAMRecord read = clipper.getRead();
ClippingData data = clipper.getData();
int readLen = read.getReadBases().length;
byte[] quals = read.getBaseQualities();
@ -338,10 +324,9 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
//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);
}
clipper.setData(data);
}
/**
@ -369,8 +354,8 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
data.nTotalBases += clipper.getRead().getReadLength();
if (clipper.wasClipped()) {
data.nClippedReads++;
data.addData(clipper.getData());
}
data.addData(clipper.getData());
return data;
}
@ -439,6 +424,13 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
nQClippedBases += data.nQClippedBases;
nRangeClippedBases += data.nRangeClippedBases;
nSeqClippedBases += data.nSeqClippedBases;
for (String seqClip : data.seqClipCounts.keySet()) {
Long count = data.seqClipCounts.get(seqClip);
if (seqClipCounts.containsKey(seqClip))
count += seqClipCounts.get(seqClip);
seqClipCounts.put(seqClip, count);
}
}
public String toString() {
@ -463,4 +455,27 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
return s.toString();
}
}
public class ReadClipperWithData extends ReadClipper {
private ClippingData data;
public ReadClipperWithData(SAMRecord read, List<SeqToClip> clipSeqs) {
super(read);
data = new ClippingData(clipSeqs);
}
public ClippingData getData() {
return data;
}
public void setData(ClippingData data) {
this.data = data;
}
public void addData(ClippingData data) {
this.data.addData(data);
}
}
}