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Removed at Mark's request. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@677 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2009-05-12 19:48:21 +00:00
parent f1de3d6366
commit ee99320c83
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java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusContextIterator.java
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package org.broadinstitute.sting.playground.gatk.iterators;
import net.sf.samtools.util.CloseableIterator;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.gatk.iterators.LocusContextIterator;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.Predicate;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.List;
import java.util.ArrayList;
import java.util.Iterator;
import edu.mit.broad.picard.filter.SamRecordFilter;
import edu.mit.broad.picard.filter.FilteringIterator;
/**
* Iterator that traverses a SAM File, accumulating information on a per-locus basis
*/
public class SingleLocusContextIterator extends LocusContextIterator {
// -----------------------------------------------------------------------------------------------------------------
//
// member fields
//
// -----------------------------------------------------------------------------------------------------------------
private final PushbackIterator<SAMRecord> it;
private String contig = null;
private int position = -1;
private List<SAMRecord> reads = new ArrayList<SAMRecord>(100);
private List<Integer> offsets = new ArrayList<Integer>(100);
// -----------------------------------------------------------------------------------------------------------------
//
// constructors and other basic operations
//
// -----------------------------------------------------------------------------------------------------------------
public SingleLocusContextIterator(final CloseableIterator<SAMRecord> samIterator) {
FilteringIterator filterIter = new FilteringIterator(samIterator, new locusStreamFilterFunc());
this.it = new PushbackIterator<SAMRecord>(filterIter);
}
/**
* Class to filter out un-handle-able reads from the stream.
*/
class locusStreamFilterFunc implements SamRecordFilter {
public boolean filterOut(SAMRecord rec) {
return rec.getCigar().numCigarElements() > 1;
}
}
public Iterator<LocusContext> iterator() {
return this;
}
public void close() {
//this.it.close();
}
public boolean hasNext() {
return it.hasNext();
}
// -----------------------------------------------------------------------------------------------------------------
//
// next() routine and associated collection operations
//
// -----------------------------------------------------------------------------------------------------------------
public LocusContext next() {
position += 1;
if ( position != -1 ) {
cleanReads();
expandReads();
}
if ( reads.isEmpty() ) {
// the window is empty, we need to jump to the first pos of the first read in the stream
SAMRecord read = it.next();
pushRead(read);
contig = read.getReferenceName();
position = read.getAlignmentStart() - 1;
return next();
}
else {
// at this point, window contains all reads covering the pos, we need to return them
// and the offsets into each read for this loci
calcOffsetsOfWindow(position);
return new LocusContext(new GenomeLoc(contig, position), reads, offsets);
}
}
private void pushRead(SAMRecord read) {
//System.out.printf(" -> Adding read %s %d-%d flags %s%n", read.getReadName(), read.getAlignmentStart(), read.getAlignmentEnd(), Utils.readFlagsAsString(read));
reads.add(read);
}
class KeepReadPFunc implements Predicate<SAMRecord> {
public boolean apply(SAMRecord read) {
return position >= read.getAlignmentStart() &&
position < read.getAlignmentEnd() &&
read.getReferenceName().equals(contig); // should be index for efficiency
}
}
Predicate KeepReadP = new SingleLocusContextIterator.KeepReadPFunc();
private void calcOffsetsOfWindow(final int position) {
offsets.clear();
for ( SAMRecord read : reads ) {
// def calcOffset( read ):
// offset = self.pos - read.start
// return offset
//
// offsets = map(calcOffset, self.window)
final int offset = position - read.getAlignmentStart();
assert(offset < read.getReadLength() );
offsets.add(offset);
//System.out.printf("offsets [%d] %s%n", read.getAlignmentStart(), offsets);
}
}
private void cleanReads() {
// def keepReadP( read ):
// return read.chr == chr and pos >= read.start and pos <= read.end
// self.window = filter( keepReadP, self.window )
reads = Utils.filter(KeepReadP, reads);
}
private void expandReads() {
// for read in self.rs:
// #print 'read', read, pos
// if read.chr == chr and read.start <= pos and read.end >= pos:
// self.pushRead(read)
// else:
// self.rs.unget( read )
// #self.rs = chain( [read], self.rs )
// break
while ( it.hasNext() ) {
SAMRecord read = it.next();
if ( KeepReadP.apply( read ) ) {
pushRead(read);
}
else {
it.pushback(read);
break;
}
}
}
public void remove() {
throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
}
}