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Merged bug fix from Stable into Unstable

This commit is contained in:
Matt Hanna 2011-09-28 21:26:43 -04:00
parent c5f1a4325f 0acaf2df65
commit 9272ed03b5
2 changed files with 39 additions and 42 deletions
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67
public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
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@ -10,6 +10,7 @@ import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Iterator;
import java.util.List;
@ -37,7 +38,7 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
/**
* The data source for reads. Will probably come directly from the BAM file.
*/
private final Iterator<AlignmentContext> sourceIterator;
private final PeekableIterator<AlignmentContext> sourceIterator;
/**
* Stores the sequence of intervals that the windowmaker should be tracking.
@ -69,7 +70,7 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
this.sourceInfo = shard.getReadProperties();
this.readIterator = iterator;
this.sourceIterator = new LocusIteratorByState(iterator,sourceInfo,genomeLocParser,sampleData);
this.sourceIterator = new PeekableIterator<AlignmentContext>(new LocusIteratorByState(iterator,sourceInfo,genomeLocParser,sampleData));
this.intervalIterator = intervals.size()>0 ? new PeekableIterator<GenomeLoc>(intervals.iterator()) : null;
}
@ -100,11 +101,6 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
*/
private final GenomeLoc locus;
/**
* Signal not to advance the iterator because we're currently sitting at the next element.
*/
private boolean atNextElement = false;
public WindowMakerIterator(GenomeLoc locus) {
this.locus = locus;
advance();
@ -124,58 +120,45 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
public boolean hasNext() {
advance();
return atNextElement;
return currentAlignmentContext != null;
}
public AlignmentContext next() {
advance();
if(!atNextElement) throw new NoSuchElementException("WindowMakerIterator is out of elements for this interval.");
if(!hasNext()) throw new NoSuchElementException("WindowMakerIterator is out of elements for this interval.");
// Prepare object state for no next element.
// Consume this alignment context.
AlignmentContext toReturn = currentAlignmentContext;
currentAlignmentContext = null;
atNextElement = false;
// Return the current element.
return toReturn;
}
private void advance() {
// No shard boundaries specified. If currentAlignmentContext has been consumed, grab the next one.
if(locus == null) {
if(!atNextElement && sourceIterator.hasNext()) {
currentAlignmentContext = sourceIterator.next();
atNextElement = true;
}
return;
}
// Can't possibly find another element. Skip out early.
if(currentAlignmentContext == null && !sourceIterator.hasNext())
return;
// Need to find the next element that is not past shard boundaries. If we travel past the edge of
// shard boundaries, stop and let the next interval pick it up.
while(sourceIterator.hasNext()) {
// Seed the current alignment context first time through the loop.
if(currentAlignmentContext == null)
currentAlignmentContext = sourceIterator.next();
while(currentAlignmentContext == null && sourceIterator.hasNext()) {
// Advance the iterator and try again.
AlignmentContext candidateAlignmentContext = sourceIterator.peek();
// Found a match.
if(locus.containsP(currentAlignmentContext.getLocation())) {
atNextElement = true;
if(locus == null) {
// No filter present. Return everything that LocusIteratorByState provides us.
currentAlignmentContext = sourceIterator.next();
}
else if(locus.isPast(candidateAlignmentContext.getLocation()))
// Found a locus before the current window; claim this alignment context and throw it away.
sourceIterator.next();
else if(locus.containsP(candidateAlignmentContext.getLocation())) {
// Found a locus within the current window; claim this alignment context and call it the next entry.
currentAlignmentContext = sourceIterator.next();
}
else if(locus.isBefore(candidateAlignmentContext.getLocation())) {
// Whoops. Skipped passed the end of the region. Iteration for this window is complete. Do
// not claim this alignment context in case it is part of the next shard.
break;
}
// Whoops. Skipped passed the end of the region. Iteration for this window is complete.
if(locus.isBefore(currentAlignmentContext.getLocation()))
break;
// No more elements to examine. Iteration is complete.
if(!sourceIterator.hasNext())
break;
// Advance the iterator and try again.
currentAlignmentContext = sourceIterator.next();
else
throw new ReviewedStingException("BUG: filtering locus does not contain, is not before, and is not past the given alignment context");
}
}
}

14
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
View File

@ -118,6 +118,20 @@ public abstract class LocusViewTemplate extends BaseTest {
testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
}
@Test
public void readAndLocusOverlapAtLastBase() {
SAMRecord read = buildSAMRecord("chr1", 1, 5);
SAMRecordIterator iterator = new SAMRecordIterator(read);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 5, 5)));
WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
WindowMaker.WindowMakerIterator window = windowMaker.next();
LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
LocusView view = createView(dataProvider);
testReadsInContext(view, shard.getGenomeLocs(), Collections.singletonList(read));
}
@Test
public void readOverlappingStartTest() {
SAMRecord read = buildSAMRecord("chr1", 1, 10);