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Haven't heard any complaints, so I'm deleting the original implementation of TraverseByLociByReference. All TbyLbyR's will now go through the new sharding code. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@637 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-08 13:37:00 +00:00
parent bae4256574
commit a5154d99a3
2 changed files with 2 additions and 133 deletions
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13
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -245,17 +245,8 @@ public class GenomeAnalysisTK extends CommandLineProgram {
Utils.scareUser(String.format("Analysis %s doesn't support SAM/BAM reads, but a read file %s was provided", Analysis_Name, INPUT_FILES));
if ( WALK_ALL_LOCI ) {
// TODO: Temporary debugging code. Activate the new debugging code only when the MicroScheduler
// is not filtered.
if( !DISABLE_THREADING ) {
logger.warn("Preliminary threading support ENABLED");
microScheduler = MicroScheduler.create( walker, INPUT_FILES, REF_FILE_ARG, rods, numThreads );
this.engine = microScheduler.getTraversalEngine();
}
else {
logger.warn("Preliminary threading support DISABLED");
this.engine = new TraverseByLociByReference(INPUT_FILES, REF_FILE_ARG, rods);
}
microScheduler = MicroScheduler.create( walker, INPUT_FILES, REF_FILE_ARG, rods, numThreads );
this.engine = microScheduler.getTraversalEngine();
}
else
this.engine = new TraverseByLoci(INPUT_FILES, REF_FILE_ARG, rods);

122
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java
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@ -1,122 +0,0 @@
package org.broadinstitute.sting.gatk.traversals;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.gatk.iterators.LocusIteratorByHanger;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import java.util.List;
import java.util.Arrays;
import java.util.Iterator;
import java.util.ArrayList;
import java.io.File;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import edu.mit.broad.picard.filter.FilteringIterator;
/**
* A simple, short-term solution to iterating over all reference positions over a series of
* genomic locations. Simply overloads the superclass traverse function to go over the entire
* interval's reference positions.
*/
public class TraverseByLociByReference extends TraverseByLoci {
public TraverseByLociByReference(List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
super(reads, ref, rods);
}
public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
//if ( locations.isEmpty() )
// Utils.scareUser("Requested all locations be processed without providing locations to be processed!");
return super.traverse(walker, locations);
}
protected <M, T> T carryWalkerOverInterval( LocusWalker<M, T> walker,
Iterator<SAMRecord> readIter,
T sum,
GenomeLoc interval ) {
logger.debug(String.format("TraverseByLociByReference.carryWalkerOverInterval Genomic interval is %s", interval));
boolean done = false;
List<SAMRecord> NO_READS = new ArrayList<SAMRecord>();
List<Integer> NO_OFFSETS = new ArrayList<Integer>();
FilteringIterator filterIter = new FilteringIterator(readIter, new locusStreamFilterFunc());
LocusIterator locusIter = new LocusIteratorByHanger(filterIter); // prepare the iterator by loci from reads
ReferenceIterator refSite = null;
LocusContext locusFromReads = null;
if( interval != null ) {
refSite = refIter.seekForward(interval); // jump to the first reference site
locusFromReads = advanceReadsToLoc(locusIter, interval); // load up the next locus by reads
}
else {
refSite = refIter.next();
locusFromReads = locusIter.next();
}
// We keep processing while the next reference location is within the interval
while ( (interval == null || interval.containsP(refSite.getLocation())) && ! done ) {
logger.debug(String.format(" LocusFromReads is %s", locusFromReads == null ? null : locusFromReads.getLocation()));
TraversalStatistics.nRecords++;
GenomeLoc current = refSite.getLocation();
// Iterate forward to get all reference ordered data covering this locus
final RefMetaDataTracker tracker = getReferenceOrderedDataAtLocus(current);
LocusContext locus = null;
if ( locusFromReads != null && locusFromReads.getLocation().compareTo(current) == 0 ) { // we are at the same site
locus = locusFromReads;
if ( locusIter.hasNext() )
locusFromReads = locusIter.next(); // advance the iterator
}
else
locus = new LocusContext(current, NO_READS, NO_OFFSETS); // make the empty locus that has no reads
locus.setReferenceContig(refSite.getCurrentContig());
if ( DOWNSAMPLE_BY_COVERAGE )
locus.downsampleToCoverage(downsamplingCoverage);
sum = walkAtLocus( walker, sum, locus, refSite, tracker );
if (this.maxReads > 0 && TraversalStatistics.nRecords > this.maxReads) {
logger.warn(String.format("Maximum number of reads encountered, terminating traversal " + TraversalStatistics.nRecords));
done = true;
}
printProgress("loci", locus.getLocation());
refSite = refIter.next(); // update our location
}
return sum;
}
private LocusContext advanceReadsToLoc(LocusIterator locusIter, GenomeLoc target) {
if ( ! locusIter.hasNext() )
return null;
LocusContext locus = locusIter.next();
while ( ! target.containsP(locus.getLocation()) && locusIter.hasNext() ) {
logger.debug(String.format(" current locus is %s vs %s => %d", locus.getLocation(), target, locus.getLocation().compareTo(target)));
locus = locusIter.next();
}
logger.debug(String.format(" returning %s", locus.getLocation()));
return locus;
}
}