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Support for reseting the system; Cleanup later 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@174 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-24 20:52:11 +00:00
parent 499c422de6
commit 9f500215da
1 changed files with 78 additions and 6 deletions
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84
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.iterators;
import net.sf.samtools.util.CloseableIterator;
import net.sf.samtools.util.RuntimeIOException;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.AlignmentBlock;
import org.broadinstitute.sting.utils.*;
@ -29,13 +30,14 @@ public class LocusIteratorByHanger extends LocusIterator {
private RefHanger<Integer> offsetHanger = new RefHanger<Integer>();
final int INCREMENT_SIZE = 100;
final boolean DEBUG = false;
boolean justCleared = false;
// -----------------------------------------------------------------------------------------------------------------
//
// constructors and other basic operations
//
// -----------------------------------------------------------------------------------------------------------------
public LocusIteratorByHanger(final CloseableIterator<SAMRecord> samIterator) {
public LocusIteratorByHanger(final Iterator<SAMRecord> samIterator) {
this.it = new PushbackIterator<SAMRecord>(samIterator);
}
@ -67,12 +69,29 @@ public class LocusIteratorByHanger extends LocusIterator {
}
}
public void clear() {
System.out.printf("clear() called%n");
readHanger.clear();
offsetHanger.clear();
}
// -----------------------------------------------------------------------------------------------------------------
//
// next() routine and associated collection operations
//
// -----------------------------------------------------------------------------------------------------------------
public LocusContext next() {
// if ( it.hasNext() && ! readHanger.isEmpty() ) {
// // todo: this needs to be deleted
// final SAMRecord read = it.peek();
// GenomeLoc readLoc = Utils.genomicLocationOf(read);
// System.out.printf("Comparing %s to %s%n", readLoc, readHanger.getLeftLoc());
// if ( readLoc.compareTo(readHanger.getLeftLoc()) == -1 ) {
// clear();
// return next();
// }
// }
if ( ! currentPositionIsFullyCovered() )
expandWindow(INCREMENT_SIZE);
@ -90,6 +109,7 @@ public class LocusIteratorByHanger extends LocusIterator {
protected void hangRead(final SAMRecord read) {
GenomeLoc readLoc = new GenomeLoc(read.getReferenceName(), read.getAlignmentStart());
//System.out.printf("Adding read %s at %d%n", read.getReadName(), read.getAlignmentStart());
/*
for ( int i = 0; i < read.getReadLength(); i++ ) {
GenomeLoc offset = new GenomeLoc(readLoc.getContig(), readLoc.getStart() + i);
@ -149,15 +169,16 @@ public class LocusIteratorByHanger extends LocusIterator {
}
SAMRecord read = it.next();
justCleared = false;
GenomeLoc readLoc = Utils.genomicLocationOf(read);
if ( DEBUG ) {
System.out.printf(" Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d%n",
readHanger.size(), incrementSize,
readHanger.hasHangers() ? readHanger.getLeftLoc() : "NA",
readHanger.hasHangers() ? readHanger.getRightLoc() : "NA",
readLoc,
readHanger.hasHangers() ? readLoc.compareTo(readHanger.getLeftLoc()) : -100);
readHanger.size(), incrementSize,
readHanger.hasHangers() ? readHanger.getLeftLoc() : "NA",
readHanger.hasHangers() ? readHanger.getRightLoc() : "NA",
readLoc,
readHanger.hasHangers() ? readLoc.compareTo(readHanger.getLeftLoc()) : -100);
}
//if ( readHanger.size() >= incrementSize ) {
//if ( readHanger.hasHangers() && readLoc.compareTo(readHanger.getLeftLoc()) == 1) {
@ -171,6 +192,57 @@ public class LocusIteratorByHanger extends LocusIterator {
}
}
// private final void expandWindow(final int incrementSize) {
// if ( DEBUG ) {
// System.out.printf("entering expandWindow..., hasNext=%b%n", it.hasNext());
// printState();
// }
//
// while ( it.hasNext() ) {
// if ( DEBUG ) {
// System.out.printf("Expanding window%n");
// printState();
// }
//
// try {
// SAMRecord read = it.next();
// justCleared = false;
//
// GenomeLoc readLoc = Utils.genomicLocationOf(read);
// if ( DEBUG ) {
// System.out.printf(" Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d%n",
// readHanger.size(), incrementSize,
// readHanger.hasHangers() ? readHanger.getLeftLoc() : "NA",
// readHanger.hasHangers() ? readHanger.getRightLoc() : "NA",
// readLoc,
// readHanger.hasHangers() ? readLoc.compareTo(readHanger.getLeftLoc()) : -100);
// }
// //if ( readHanger.size() >= incrementSize ) {
// //if ( readHanger.hasHangers() && readLoc.compareTo(readHanger.getLeftLoc()) == 1) {
// if ( readHanger.hasHangers() && readLoc.distance(readHanger.getLeftLoc()) >= incrementSize ) {
// // We've collected up enough reads
// it.pushback(read);
// break;
// }
// else
// hangRead(read);
// }
// catch ( RuntimeIOException rio ) {
// System.out.printf("Clearing state...");
// // todo: good god, this is dangerous, we are reseting state because the reads are out of order
// if ( ! justCleared ) {
// rio.printStackTrace();
// justCleared = true;
// clear();
// }
// it.next(); // throw away the offending read
// expandWindow(INCREMENT_SIZE);
// return;
// }
// }
// }
public void remove() {
throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
}