zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Partially reclaim performance lost during integration test fixes. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2961 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-09 12:36:11 +00:00
parent 9f3b99c11b
commit cdce639bae
1 changed files with 21 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

29
java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
View File

@ -4,10 +4,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.Reads;
import java.util.List;
import java.util.Queue;
import java.util.ArrayDeque;
import java.util.Iterator;
import java.util.*;
import net.sf.samtools.SAMRecord;
import net.sf.picard.util.PeekableIterator;
@ -21,10 +18,15 @@ import net.sf.picard.util.PeekableIterator;
* @version 0.1
*/
public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, Iterator<WindowMaker.WindowMakerIterator> {
/**
* Source information for iteration.
*/
private final Reads sourceInfo;
/**
* The data source for reads. Will probably come directly from the BAM file.
*/
private final StingSAMIterator sourceIterator;
private final PeekableIterator<SAMRecord> sourceIterator;
/**
* Stores the sequence of intervals that the windowmaker should be tracking.
@ -43,7 +45,8 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
* @param intervals The set of intervals over which to traverse.
*/
public WindowMaker(StingSAMIterator iterator, List<GenomeLoc> intervals) {
this.sourceIterator = iterator;
this.sourceInfo = iterator.getSourceInfo();
this.sourceIterator = new PeekableIterator<SAMRecord>(iterator);
this.intervalIterator = new PeekableIterator<GenomeLoc>(intervals.iterator());
}
@ -83,7 +86,7 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
}
public Reads getSourceInfo() {
return sourceIterator.getSourceInfo();
return sourceInfo;
}
public GenomeLoc getLocus() {
@ -95,10 +98,20 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
}
public boolean hasNext() {
return overlappingReads.size() > 0 || sourceIterator.hasNext();
if(overlappingReads.size() > 0) return true;
if(sourceIterator.hasNext()) {
SAMRecord nextRead = sourceIterator.peek();
if((nextRead.getAlignmentStart() >= locus.getStart() && nextRead.getAlignmentStart() <= locus.getStop()) ||
(nextRead.getAlignmentEnd() >= locus.getStart() && nextRead.getAlignmentEnd() <= locus.getStop()) ||
(nextRead.getAlignmentStart() < locus.getStart() && nextRead.getAlignmentEnd() > locus.getStop()))
return true;
}
return false;
}
public SAMRecord next() {
if(!hasNext()) throw new NoSuchElementException("WindowMakerIterator is out of elements for this interval.");
SAMRecord nextRead = overlappingReads.size() > 0 ? overlappingReads.remove() : sourceIterator.next();
if(intervalIterator.hasNext() && nextRead.getAlignmentEnd() >= intervalIterator.peek().getStart())
pendingOverlaps.add(nextRead);