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Clean up the code a bit following the introduction of reduceByInterval. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2887 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-02-25 01:20:22 +00:00
parent 199b43fcf2
commit 553d39bb00
4 changed files with 16 additions and 51 deletions
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2
java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
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@ -47,7 +47,7 @@ public class AllLocusView extends LocusView {
public AllLocusView(ShardDataProvider provider) {
super( provider );
// Seed the state tracking members with the first possible seek position and the first possible locus context.
locusIterator = new GenomeLocusIterator( Collections.singletonList(provider.getLocus()) );
locusIterator = new GenomeLocusIterator(provider.getLocus());
if( locusIterator.hasNext() ) {
nextPosition = locusIterator.next();
nextLocus = hasNextLocus() ? nextLocus() : createEmptyLocus(nextPosition);

15
java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
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@ -66,20 +66,7 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
throw new StingException("Cannot power an IndexDelimitedLocusShardStrategy with this data source.");
blockDrivenDataSource = (BlockDrivenSAMDataSource)dataSource;
// Create a list of contig name -> genome loc, sorted in INSERTION ORDER.
LinkedHashMap<String,List<GenomeLoc>> locationToReference = new LinkedHashMap<String,List<GenomeLoc>>();
for(GenomeLoc location: locations) {
if(!locationToReference.containsKey(location.getContig()))
locationToReference.put(location.getContig(),new ArrayList<GenomeLoc>());
locationToReference.get(location.getContig()).add(location);
}
// TODO: Not sure there's any reason to pre-separate the contigs now that we're using a streaming approach to file pointer allocation.
for(String contig: locationToReference.keySet()) {
filePointers.addAll(batchLociIntoBins(locationToReference.get(contig),blockDrivenDataSource.getNumIndexLevels()-1));
}
filePointers.addAll(batchLociIntoBins(locations.toList(),blockDrivenDataSource.getNumIndexLevels()-1));
filePointerIterator = filePointers.iterator();
}

46
java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
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@ -5,7 +5,6 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.NoSuchElementException;
import java.util.Iterator;
import java.util.List;
/**
* User: hanna
* Date: May 12, 2009
@ -24,28 +23,24 @@ import java.util.List;
*/
public class GenomeLocusIterator implements Iterator<GenomeLoc> {
/**
* An iterator to the entire data structure over which we're iterating.
* The entire region over which we're iterating.
*/
private final Iterator<GenomeLoc> locusIterator;
private GenomeLoc completeLocus;
/**
* The multi-base pair long locus referring to the current locus.
* The current position in the traversal.
*/
private GenomeLoc currentLocus = null;
/**
* The 1 base pair long location.
*/
private GenomeLoc currentLocation = null;
private GenomeLoc currentLocus;
/**
* Creates an iterator that can traverse over the entire
* reference specified in the given ShardDataProvider.
* @param loci the list of loci over which to iterate.
* @param completeLocus Data provider to use as a backing source.
* Provider must have a reference (hasReference() == true).
*/
public GenomeLocusIterator( List<GenomeLoc> loci ) {
this.locusIterator = loci.iterator();
seedNextLocus();
public GenomeLocusIterator( GenomeLoc completeLocus ) {
this.completeLocus = completeLocus;
this.currentLocus = GenomeLocParser.createGenomeLoc(completeLocus.getContig(),completeLocus.getStart());
}
/**
@ -53,7 +48,7 @@ public class GenomeLocusIterator implements Iterator<GenomeLoc> {
* @return True if the iterator has more elements. False otherwise.
*/
public boolean hasNext() {
return currentLocation != null;
return !currentLocus.isPast(completeLocus);
}
/**
@ -63,29 +58,12 @@ public class GenomeLocusIterator implements Iterator<GenomeLoc> {
public GenomeLoc next() {
if( !hasNext() )
throw new NoSuchElementException("No elements remaining in bounded reference region.");
GenomeLoc toReturn = currentLocation.clone();
seedNextLocus();
GenomeLoc toReturn = (GenomeLoc)currentLocus.clone();
currentLocus = GenomeLocParser.incPos(currentLocus);
return toReturn;
}
public void remove() {
throw new UnsupportedOperationException( "ReferenceLocusIterator is read-only" );
}
/**
* Position currentLocation at the next locus, if possible.
*/
private void seedNextLocus() {
if(currentLocus != null && currentLocation != null)
currentLocation = GenomeLocParser.incPos(currentLocation);
// If initializing or the location was pushed off the current locus, reinitialize using the next locus.
if(currentLocus == null || currentLocation == null || currentLocation.isPast(currentLocus)) {
currentLocus = currentLocation = null;
if(locusIterator.hasNext()){
currentLocus = locusIterator.next();
currentLocation = GenomeLocParser.createGenomeLoc(currentLocus.getContig(),currentLocus.getStart());
}
}
}
}

4
java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java
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@ -89,9 +89,9 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
*/
protected void validateLocation( GenomeLoc loc ) {
Shard shard = new LocusShard(Collections.singletonList(loc));
GenomeLocusIterator shardIterator = new GenomeLocusIterator(shard.getGenomeLocs());
GenomeLocusIterator shardIterator = new GenomeLocusIterator(loc);
ShardDataProvider dataProvider = new ShardDataProvider(shard, shard.getGenomeLocs().get(0), null, sequenceFile, null);
ShardDataProvider dataProvider = new ShardDataProvider(shard, loc, null, sequenceFile, null);
LocusReferenceView view = new LocusReferenceView(dataProvider);
while (shardIterator.hasNext()) {