Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Mark DePristo
commit
fd37da13af
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@ -333,10 +333,6 @@ public class RefMetaDataTracker {
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return addValues(name, type, new ArrayList<T>(), getTrackDataByName(name), onlyAtThisLoc, true, false);
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}
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@Deprecated
|
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public <T extends Feature> List<T> getValues(final Class<T> type, final Collection<String> names, final GenomeLoc onlyAtThisLoc) {
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return addValues(names, type, new ArrayList<T>(), onlyAtThisLoc, true, false);
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}
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@Deprecated
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public <T extends Feature> T getFirstValue(final Class<T> type, final String name) {
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return safeGetFirst(getValues(type, name));
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}
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|
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@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation;
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import org.broadinstitute.sting.utils.clipreads.ReadClipper;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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import org.yaml.snakeyaml.events.SequenceStartEvent;
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import java.io.File;
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import java.io.PrintStream;
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@ -54,7 +55,7 @@ import java.util.regex.Pattern;
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* with poor quality scores, that match particular sequences, or that were generated by particular machine cycles.
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*/
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@Requires({DataSource.READS})
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public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.ClippingData> {
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public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithData, ClipReadsWalker.ClippingData> {
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@Output
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PrintStream out;
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@ -180,12 +181,12 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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* @param read the read itself, as a SAMRecord
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* @return the ReadClipper object describing what should be done to clip this read
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*/
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public ReadClipper map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
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public ReadClipperWithData map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
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if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
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if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES ) {
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read = ReadUtils.replaceSoftClipsWithMatches(read);
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}
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ReadClipper clipper = new ReadClipper(read);
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ReadClipperWithData clipper = new ReadClipperWithData(read, sequencesToClip);
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//
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// run all three clipping modules
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@ -205,9 +206,10 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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*
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* @param clipper
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*/
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private void clipSequences(ReadClipper clipper) {
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private void clipSequences(ReadClipperWithData clipper) {
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if (sequencesToClip != null) { // don't bother if we don't have any sequences to clip
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SAMRecord read = clipper.getRead();
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ClippingData data = clipper.getData();
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for (SeqToClip stc : sequencesToClip) {
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// we have a pattern for both the forward and the reverse strands
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@ -223,11 +225,14 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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if (found) {
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int start = match.start();
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int stop = match.end() - 1;
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ClippingOp op = new ClippingOp(ClippingOp.ClippingType.MATCHES_CLIP_SEQ, start, stop, stc.seq);
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//ClippingOp op = new ClippingOp(ClippingOp.ClippingType.MATCHES_CLIP_SEQ, start, stop, stc.seq);
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ClippingOp op = new ClippingOp(start, stop);
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clipper.addOp(op);
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data.incSeqClippedBases(stc.seq, op.getLength());
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}
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}
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}
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clipper.setData(data);
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}
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}
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@ -252,9 +257,10 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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*
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* @param clipper
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*/
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private void clipCycles(ReadClipper clipper) {
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private void clipCycles(ReadClipperWithData clipper) {
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if (cyclesToClip != null) {
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SAMRecord read = clipper.getRead();
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ClippingData data = clipper.getData();
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for (Pair<Integer, Integer> p : cyclesToClip) { // iterate over each cycle range
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int cycleStart = p.first;
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@ -270,10 +276,13 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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int start = startStop.first;
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int stop = startStop.second;
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ClippingOp op = new ClippingOp(ClippingOp.ClippingType.WITHIN_CLIP_RANGE, start, stop, null);
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//ClippingOp op = new ClippingOp(ClippingOp.ClippingType.WITHIN_CLIP_RANGE, start, stop, null);
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ClippingOp op = new ClippingOp(start, stop);
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clipper.addOp(op);
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data.incNRangeClippedBases(op.getLength());
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}
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}
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clipper.setData(data);
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}
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}
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@ -291,8 +300,9 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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*
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* @param clipper
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*/
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private void clipBadQualityScores(ReadClipper clipper) {
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private void clipBadQualityScores(ReadClipperWithData clipper) {
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SAMRecord read = clipper.getRead();
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ClippingData data = clipper.getData();
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int readLen = read.getReadBases().length;
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byte[] quals = read.getBaseQualities();
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|
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@ -311,8 +321,12 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
|
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if (clipPoint != -1) {
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int start = read.getReadNegativeStrandFlag() ? 0 : clipPoint;
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int stop = read.getReadNegativeStrandFlag() ? clipPoint : readLen - 1;
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clipper.addOp(new ClippingOp(ClippingOp.ClippingType.LOW_Q_SCORES, start, stop, null));
|
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//clipper.addOp(new ClippingOp(ClippingOp.ClippingType.LOW_Q_SCORES, start, stop, null));
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ClippingOp op = new ClippingOp(start, stop);
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clipper.addOp(op);
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data.incNQClippedBases(op.getLength());
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}
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clipper.setData(data);
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}
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/**
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@ -325,7 +339,7 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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return new ClippingData(sequencesToClip);
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}
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public ClippingData reduce(ReadClipper clipper, ClippingData data) {
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public ClippingData reduce(ReadClipperWithData clipper, ClippingData data) {
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if ( clipper == null )
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return data;
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@ -340,23 +354,8 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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data.nTotalBases += clipper.getRead().getReadLength();
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if (clipper.wasClipped()) {
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data.nClippedReads++;
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for (ClippingOp op : clipper.getOps()) {
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switch (op.type) {
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case LOW_Q_SCORES:
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data.incNQClippedBases(op.getLength());
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break;
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case WITHIN_CLIP_RANGE:
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data.incNRangeClippedBases(op.getLength());
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break;
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case MATCHES_CLIP_SEQ:
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data.incSeqClippedBases((String) op.extraInfo, op.getLength());
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break;
|
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default:
|
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throw new IllegalStateException("Unexpected Clipping operator type " + op);
|
||||
}
|
||||
}
|
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data.addData(clipper.getData());
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}
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|
||||
return data;
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||||
}
|
||||
|
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@ -417,6 +416,23 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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seqClipCounts.put(seq, seqClipCounts.get(seq) + n);
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}
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public void addData (ClippingData data) {
|
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nTotalReads += data.nTotalReads;
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nTotalBases += data.nTotalBases;
|
||||
nClippedReads += data.nClippedReads;
|
||||
nClippedBases += data.nClippedBases;
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nQClippedBases += data.nQClippedBases;
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nRangeClippedBases += data.nRangeClippedBases;
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nSeqClippedBases += data.nSeqClippedBases;
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|
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for (String seqClip : data.seqClipCounts.keySet()) {
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Long count = data.seqClipCounts.get(seqClip);
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if (seqClipCounts.containsKey(seqClip))
|
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count += seqClipCounts.get(seqClip);
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seqClipCounts.put(seqClip, count);
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}
|
||||
}
|
||||
|
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public String toString() {
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StringBuilder s = new StringBuilder();
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|
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@ -439,4 +455,27 @@ public class ClipReadsWalker extends ReadWalker<ReadClipper, ClipReadsWalker.Cli
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return s.toString();
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||||
}
|
||||
}
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|
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public class ReadClipperWithData extends ReadClipper {
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private ClippingData data;
|
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public ReadClipperWithData(SAMRecord read, List<SeqToClip> clipSeqs) {
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super(read);
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data = new ClippingData(clipSeqs);
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}
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|
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public ClippingData getData() {
|
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return data;
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}
|
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public void setData(ClippingData data) {
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this.data = data;
|
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}
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public void addData(ClippingData data) {
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this.data.addData(data);
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}
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}
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||||
}
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@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.collections.Pair;
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||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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||||
|
||||
import java.util.Collections;
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||||
import java.util.List;
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||||
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@ -49,7 +50,7 @@ import java.util.List;
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public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
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@Input(fullName = "variant", shortName = "V", doc="variants to model", required=false)
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public List<RodBinding<VariantContext>> variants;
|
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public List<RodBinding<VariantContext>> variants = Collections.emptyList();
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@Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
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public RodBinding<VariantContext> snpmask;
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@ -66,17 +67,18 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
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String refBase = String.valueOf((char)ref.getBase());
|
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|
||||
// Check to see if we have a called snp
|
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for ( VariantContext vc : tracker.getValues(VariantContext.class) ) {
|
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if ( ! vc.getSource().equals(snpmask.getName())) {
|
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if ( vc.isDeletion()) {
|
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deletionBasesRemaining = vc.getReference().length();
|
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// delete the next n bases, not this one
|
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return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
|
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} else if ( vc.isInsertion()) {
|
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return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString()));
|
||||
} else if (vc.isSNP()) {
|
||||
return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());
|
||||
}
|
||||
for ( VariantContext vc : tracker.getValues(variants) ) {
|
||||
if ( vc.isFiltered() )
|
||||
continue;
|
||||
|
||||
if ( vc.isDeletion()) {
|
||||
deletionBasesRemaining = vc.getReference().length();
|
||||
// delete the next n bases, not this one
|
||||
return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
|
||||
} else if ( vc.isInsertion()) {
|
||||
return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString()));
|
||||
} else if (vc.isSNP()) {
|
||||
return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -2,16 +2,18 @@ package org.broadinstitute.sting.gatk.walkers.qc;
|
|||
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
import org.broadinstitute.sting.commandline.Input;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.commandline.RodBinding;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
|
||||
import org.broadinstitute.sting.gatk.walkers.RefWalker;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.collections.Pair;
|
||||
|
||||
import java.io.PrintStream;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
|
|
@ -23,6 +25,9 @@ public class CountIntervals extends RefWalker<Long, Long> {
|
|||
@Output
|
||||
PrintStream out;
|
||||
|
||||
@Input(fullName="check", shortName = "check", doc="Any number of RODs", required=false)
|
||||
public List<RodBinding<Feature>> features = Collections.emptyList();
|
||||
|
||||
@Argument(fullName="numOverlaps",shortName="no",doc="Count all occurrences of X or more overlapping intervals; defaults to 2", required=false)
|
||||
int numOverlaps = 2;
|
||||
|
||||
|
|
@ -37,7 +42,7 @@ public class CountIntervals extends RefWalker<Long, Long> {
|
|||
return null;
|
||||
}
|
||||
|
||||
List<Feature> checkIntervals = tracker.getValues(Feature.class, "check");
|
||||
List<Feature> checkIntervals = tracker.getValues(features);
|
||||
return (long) checkIntervals.size();
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -4,6 +4,8 @@ import net.sf.samtools.Cigar;
|
|||
import net.sf.samtools.CigarElement;
|
||||
import net.sf.samtools.CigarOperator;
|
||||
import net.sf.samtools.SAMRecord;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.sam.ReadUtils;
|
||||
|
||||
import java.util.Vector;
|
||||
|
|
@ -16,22 +18,14 @@ import java.util.Vector;
|
|||
* according to the wishes of the supplid ClippingAlgorithm enum.
|
||||
*/
|
||||
public class ClippingOp {
|
||||
public final ClippingType type;
|
||||
public final int start, stop; // inclusive
|
||||
public final Object extraInfo;
|
||||
|
||||
public ClippingOp(int start, int stop) {
|
||||
this(null, start, stop, null);
|
||||
}
|
||||
|
||||
public ClippingOp(ClippingType type, int start, int stop, Object extraInfo) {
|
||||
// todo -- remove type and extra info
|
||||
this.type = type;
|
||||
this.start = start;
|
||||
this.stop = stop;
|
||||
this.extraInfo = extraInfo;
|
||||
}
|
||||
|
||||
|
||||
public int getLength() {
|
||||
return stop - start + 1;
|
||||
}
|
||||
|
|
@ -72,48 +66,45 @@ public class ClippingOp {
|
|||
break;
|
||||
case HARDCLIP_BASES:
|
||||
case SOFTCLIP_BASES:
|
||||
if ( ! clippedRead.getReadUnmappedFlag() ) {
|
||||
if ( clippedRead.getReadUnmappedFlag() ) {
|
||||
// we can't process unmapped reads
|
||||
|
||||
//System.out.printf("%d %d %d%n", stop, start, clippedRead.getReadLength());
|
||||
int myStop = stop;
|
||||
if ( (stop + 1 - start) == clippedRead.getReadLength() ) {
|
||||
// BAM representation issue -- we can't SOFTCLIP away all bases in a read, just leave it alone
|
||||
//Walker.logger.info(String.format("Warning, read %s has all bases clip but this can't be represented with SOFTCLIP_BASES, just leaving it alone", clippedRead.getReadName()));
|
||||
//break;
|
||||
myStop--; // just decrement stop
|
||||
}
|
||||
|
||||
if ( start > 0 && myStop != clippedRead.getReadLength() - 1 )
|
||||
throw new RuntimeException(String.format("Cannot apply soft clipping operator to the middle of a read: %s to be clipped at %d-%d",
|
||||
clippedRead.getReadName(), start, myStop));
|
||||
|
||||
Cigar oldCigar = clippedRead.getCigar();
|
||||
|
||||
int scLeft = 0, scRight = clippedRead.getReadLength();
|
||||
if ( start == 0 )
|
||||
scLeft = myStop + 1;
|
||||
else
|
||||
scRight = start;
|
||||
|
||||
Cigar newCigar = softClip(oldCigar, scLeft, scRight);
|
||||
clippedRead.setCigar(newCigar);
|
||||
|
||||
int newClippedStart = getNewAlignmentStartOffset(newCigar, oldCigar);
|
||||
int newStart = clippedRead.getAlignmentStart() + newClippedStart;
|
||||
clippedRead.setAlignmentStart(newStart);
|
||||
|
||||
if ( algorithm == ClippingRepresentation.HARDCLIP_BASES )
|
||||
clippedRead = ReadUtils.hardClipSoftClippedBases(clippedRead);
|
||||
//System.out.printf("%s clipping at %d %d / %d %d => %s and %d%n", oldCigar.toString(), start, stop, scLeft, scRight, newCigar.toString(), newStart);
|
||||
} else if ( algorithm == ClippingRepresentation.HARDCLIP_BASES ) {
|
||||
// we can hard clip unmapped reads
|
||||
if ( clippedRead.getReadNegativeStrandFlag() )
|
||||
clippedRead = ReadUtils.hardClipBases(clippedRead, 0, start, null);
|
||||
else
|
||||
clippedRead = ReadUtils.hardClipBases(clippedRead, start, start + getLength(), null);
|
||||
throw new UserException("Read Clipper cannot soft/hard clip unmapped reads");
|
||||
}
|
||||
|
||||
//System.out.printf("%d %d %d%n", stop, start, clippedRead.getReadLength());
|
||||
int myStop = stop;
|
||||
if ( (stop + 1 - start) == clippedRead.getReadLength() ) {
|
||||
// BAM representation issue -- we can't SOFTCLIP away all bases in a read, just leave it alone
|
||||
//Walker.logger.info(String.format("Warning, read %s has all bases clip but this can't be represented with SOFTCLIP_BASES, just leaving it alone", clippedRead.getReadName()));
|
||||
//break;
|
||||
myStop--; // just decrement stop
|
||||
}
|
||||
|
||||
if ( start > 0 && myStop != clippedRead.getReadLength() - 1 )
|
||||
throw new RuntimeException(String.format("Cannot apply soft clipping operator to the middle of a read: %s to be clipped at %d-%d",
|
||||
clippedRead.getReadName(), start, myStop));
|
||||
|
||||
Cigar oldCigar = clippedRead.getCigar();
|
||||
|
||||
int scLeft = 0, scRight = clippedRead.getReadLength();
|
||||
if ( start == 0 )
|
||||
scLeft = myStop + 1;
|
||||
else
|
||||
scRight = start;
|
||||
|
||||
Cigar newCigar = softClip(oldCigar, scLeft, scRight);
|
||||
clippedRead.setCigar(newCigar);
|
||||
|
||||
int newClippedStart = getNewAlignmentStartOffset(newCigar, oldCigar);
|
||||
int newStart = clippedRead.getAlignmentStart() + newClippedStart;
|
||||
clippedRead.setAlignmentStart(newStart);
|
||||
|
||||
if ( algorithm == ClippingRepresentation.HARDCLIP_BASES )
|
||||
clippedRead = ReadUtils.hardClipSoftClippedBases(clippedRead);
|
||||
//System.out.printf("%s clipping at %d %d / %d %d => %s and %d%n", oldCigar.toString(), start, stop, scLeft, scRight, newCigar.toString(), newStart);
|
||||
|
||||
break;
|
||||
|
||||
default:
|
||||
throw new IllegalStateException("Unexpected Clipping operator type " + algorithm);
|
||||
}
|
||||
|
|
@ -121,15 +112,6 @@ public class ClippingOp {
|
|||
return clippedRead;
|
||||
}
|
||||
|
||||
/**
|
||||
* What is the type of a ClippingOp?
|
||||
*/
|
||||
public enum ClippingType {
|
||||
LOW_Q_SCORES,
|
||||
WITHIN_CLIP_RANGE,
|
||||
MATCHES_CLIP_SEQ
|
||||
}
|
||||
|
||||
/**
|
||||
* Given a cigar string, get the number of bases hard or soft clipped at the start
|
||||
*/
|
||||
|
|
@ -198,7 +180,7 @@ public class ClippingOp {
|
|||
Vector<CigarElement> newElements = new Vector<CigarElement>();
|
||||
for (CigarElement curElem : __cigar.getCigarElements()) {
|
||||
if (!curElem.getOperator().consumesReadBases()) {
|
||||
if (curLength > __startClipEnd && curLength < __endClipBegin) {
|
||||
if (curElem.getOperator() == CigarOperator.HARD_CLIP || curLength > __startClipEnd && curLength < __endClipBegin) {
|
||||
newElements.add(new CigarElement(curElem.getLength(), curElem.getOperator()));
|
||||
}
|
||||
continue;
|
||||
|
|
|
|||
|
|
@ -1,6 +1,10 @@
|
|||
package org.broadinstitute.sting.utils.clipreads;
|
||||
|
||||
import net.sf.samtools.Cigar;
|
||||
import net.sf.samtools.CigarElement;
|
||||
import net.sf.samtools.SAMRecord;
|
||||
import org.broadinstitute.sting.utils.sam.ReadUtils;
|
||||
import org.jets3t.service.multi.ThreadedStorageService;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
|
@ -43,6 +47,23 @@ public class ReadClipper {
|
|||
return read;
|
||||
}
|
||||
|
||||
public SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) {
|
||||
int start = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
|
||||
int stop = ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
|
||||
this.addOp(new ClippingOp(start, stop));
|
||||
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
|
||||
}
|
||||
|
||||
public SAMRecord hardClipByReadCoordinates(int start, int stop) {
|
||||
this.addOp(new ClippingOp(start, stop));
|
||||
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
|
||||
}
|
||||
|
||||
public SAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
|
||||
this.read = hardClipByReferenceCoordinates(read.getUnclippedStart(), left);
|
||||
this.ops = null; // reset the operations
|
||||
return hardClipByReferenceCoordinates(right, read.getUnclippedEnd());
|
||||
}
|
||||
|
||||
/**
|
||||
* Return a new read corresponding to this.read that's been clipped according to ops, if any are present.
|
||||
|
|
|
|||
|
|
@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.sam;
|
|||
import com.google.java.contract.Ensures;
|
||||
import com.google.java.contract.Requires;
|
||||
import net.sf.samtools.*;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.collections.Pair;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
|
||||
|
|
@ -112,7 +113,42 @@ public class ReadUtils {
|
|||
* @version 0.1
|
||||
*/
|
||||
|
||||
public enum OverlapType { NOT_OVERLAPPING, IN_ADAPTOR }
|
||||
public enum OverlapType { NOT_OVERLAPPING, IN_ADAPTOR}
|
||||
|
||||
/**
|
||||
* This enum represents all the different ways in which a read can overlap an interval.
|
||||
*
|
||||
* NO_OVERLAP:
|
||||
* the read does not overlap the interval.
|
||||
*
|
||||
* |----------------| (interval)
|
||||
* <----------------> (read)
|
||||
*
|
||||
* LEFT_OVERLAP:
|
||||
* the read starts before the beginning of the interval but ends inside of it
|
||||
*
|
||||
* |----------------| (interval)
|
||||
* <----------------> (read)
|
||||
*
|
||||
* RIGHT_OVERLAP:
|
||||
* the read starts inside the interval but ends outside of it
|
||||
*
|
||||
* |----------------| (interval)
|
||||
* <----------------> (read)
|
||||
*
|
||||
* FULL_OVERLAP:
|
||||
* the read starts before the interval and ends after the interval
|
||||
*
|
||||
* |-----------| (interval)
|
||||
* <-------------------> (read)
|
||||
*
|
||||
* CONTAINED:
|
||||
* the read starts and ends inside the interval
|
||||
*
|
||||
* |----------------| (interval)
|
||||
* <--------> (read)
|
||||
*/
|
||||
public enum ReadAndIntervalOverlap {NO_OVERLAP, LEFT_OVERLAP, RIGHT_OVERLAP, FULL_OVERLAP, CONTAINED}
|
||||
|
||||
/**
|
||||
* God, there's a huge information asymmetry in SAM format:
|
||||
|
|
@ -396,16 +432,34 @@ public class ReadUtils {
|
|||
keepEnd = rec.getReadLength() - l - 1;
|
||||
newCigarElements.add(new CigarElement(l, CigarOperator.HARD_CLIP));
|
||||
break;
|
||||
case H:
|
||||
// TODO -- must be handled specially
|
||||
throw new ReviewedStingException("BUG: tell mark he forgot to implement this");
|
||||
|
||||
default:
|
||||
newCigarElements.add(ce);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
return hardClipBases(rec, keepStart, keepEnd, newCigarElements);
|
||||
// Merges tandem cigar elements like 5H10H or 2S5S to 15H or 7S
|
||||
// this will happen if you soft clip a read that has been hard clipped before
|
||||
// like: 5H20S => 5H20H
|
||||
List<CigarElement> mergedCigarElements = new LinkedList<CigarElement>();
|
||||
Iterator<CigarElement> cigarElementIterator = newCigarElements.iterator();
|
||||
CigarOperator currentOperator = null;
|
||||
int currentOperatorLength = 0;
|
||||
while (cigarElementIterator.hasNext()) {
|
||||
CigarElement cigarElement = cigarElementIterator.next();
|
||||
if (currentOperator != cigarElement.getOperator()) {
|
||||
if (currentOperator != null)
|
||||
mergedCigarElements.add(new CigarElement(currentOperatorLength, currentOperator));
|
||||
currentOperator = cigarElement.getOperator();
|
||||
currentOperatorLength = cigarElement.getLength();
|
||||
}
|
||||
else
|
||||
currentOperatorLength += cigarElement.getLength();
|
||||
}
|
||||
mergedCigarElements.add(new CigarElement(currentOperatorLength, currentOperator));
|
||||
|
||||
return hardClipBases(rec, keepStart, keepEnd, mergedCigarElements);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -424,8 +478,7 @@ public class ReadUtils {
|
|||
"keepEnd < rec.getReadLength()",
|
||||
"rec.getReadUnmappedFlag() || newCigarElements != null"})
|
||||
@Ensures("result != null")
|
||||
public static SAMRecord hardClipBases(SAMRecord rec, int keepStart, int keepEnd,
|
||||
List<CigarElement> newCigarElements) {
|
||||
public static SAMRecord hardClipBases(SAMRecord rec, int keepStart, int keepEnd, List<CigarElement> newCigarElements) {
|
||||
int newLength = keepEnd - keepStart + 1;
|
||||
if ( newLength != rec.getReadLength() ) {
|
||||
try {
|
||||
|
|
@ -569,7 +622,71 @@ public class ReadUtils {
|
|||
return 0;
|
||||
}
|
||||
|
||||
/**
|
||||
* Determines what is the position of the read in relation to the interval.
|
||||
* Note: This function uses the UNCLIPPED ENDS of the reads for the comparison.
|
||||
* @param read the read
|
||||
* @param interval the interval
|
||||
* @return the overlap type as described by ReadAndIntervalOverlap enum (see above)
|
||||
*/
|
||||
public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(SAMRecord read, GenomeLoc interval) {
|
||||
if ( (!read.getReferenceName().equals(interval.getContig())) ||
|
||||
(read.getUnclippedEnd() < interval.getStart()) ||
|
||||
(read.getUnclippedStart() > interval.getStop()) )
|
||||
return ReadAndIntervalOverlap.NO_OVERLAP;
|
||||
|
||||
else if ( (read.getUnclippedStart() >= interval.getStart()) &&
|
||||
(read.getUnclippedEnd() <= interval.getStop()) )
|
||||
return ReadAndIntervalOverlap.CONTAINED;
|
||||
|
||||
else if ( (read.getUnclippedStart() < interval.getStart()) &&
|
||||
(read.getUnclippedEnd() > interval.getStop()) )
|
||||
return ReadAndIntervalOverlap.FULL_OVERLAP;
|
||||
|
||||
else if ( (read.getAlignmentStart() < interval.getStart()) )
|
||||
return ReadAndIntervalOverlap.LEFT_OVERLAP;
|
||||
|
||||
else
|
||||
return ReadAndIntervalOverlap.RIGHT_OVERLAP;
|
||||
}
|
||||
|
||||
@Requires({"refCoord >= read.getUnclippedStart()", "refCoord <= read.getUnclippedEnd()"})
|
||||
@Ensures({"result >= 0", "result < read.getReadLength()"})
|
||||
public static int getReadCoordinateForReferenceCoordinate(SAMRecord read, int refCoord) {
|
||||
int readBases = 0;
|
||||
int refBases = 0;
|
||||
int goal = refCoord - read.getUnclippedStart(); // read coords are 0-based!
|
||||
boolean goalReached = false;
|
||||
|
||||
Iterator<CigarElement> cigarElementIterator = read.getCigar().getCigarElements().iterator();
|
||||
while (!goalReached && cigarElementIterator.hasNext()) {
|
||||
CigarElement cigarElement = cigarElementIterator.next();
|
||||
int shift = 0;
|
||||
if (refBases == 0 && readBases == 0 && cigarElement.getOperator() == CigarOperator.HARD_CLIP) {
|
||||
goal -= cigarElement.getLength();
|
||||
}
|
||||
|
||||
if (cigarElement.getOperator().consumesReferenceBases()) {
|
||||
if (refBases + cigarElement.getLength() < goal) {
|
||||
shift = cigarElement.getLength();
|
||||
}
|
||||
else {
|
||||
shift = goal - refBases;
|
||||
}
|
||||
refBases += shift;
|
||||
}
|
||||
goalReached = refBases == goal;
|
||||
|
||||
if (cigarElement.getOperator().consumesReadBases()) {
|
||||
readBases += goalReached ? shift : cigarElement.getLength();
|
||||
}
|
||||
}
|
||||
|
||||
if (!goalReached)
|
||||
throw new ReviewedStingException("Somehow the requested coordinate is not covered by the read. Too many deletions?");
|
||||
|
||||
return readBases;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue