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Stop using the annoying refIterator (temp change until new traversal is green lighted) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1103 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-25 20:05:39 +00:00
parent 0c3aabd1c5
commit 83816fb801
1 changed files with 17 additions and 38 deletions
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55
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
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@ -2,19 +2,15 @@ package org.broadinstitute.sting.gatk.traversals;
import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.Reads;
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.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.fasta.*;
import java.util.*;
import java.io.File;
import java.io.*;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileReader;
@ -31,6 +27,8 @@ import net.sf.picard.sam.SamFileHeaderMerger;
*/
public class TraverseByLocusWindows extends TraversalEngine {
private IndexedFastaSequenceFile sequenceFile = null;
public TraverseByLocusWindows(List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
super(reads, ref, rods);
}
@ -62,6 +60,13 @@ public class TraverseByLocusWindows extends TraversalEngine {
if(readsFiles.size() > 1)
throw new UnsupportedOperationException("Cannot do ByInterval traversal on file with multiple inputs.");
try {
sequenceFile = new IndexedFastaSequenceFile(GenomeAnalysisEngine.instance.getArguments().referenceFile);
}
catch ( FileNotFoundException ex ) {
throw new StingException("No ref!",ex);
}
samReader = initializeSAMFile(readsFiles.get(0));
verifySortOrder(true);
@ -127,40 +132,14 @@ public class TraverseByLocusWindows extends TraversalEngine {
return locus;
}
private LocusContext merge(LocusContext locus1, LocusContext locus2) {
GenomeLoc loc = locus1.getLocation().merge(locus2.getLocation());
TreeSet<SAMRecord> set = new TreeSet<SAMRecord>(new Comparator<SAMRecord>() {
public int compare(SAMRecord obj1, SAMRecord obj2) {
GenomeLoc myLoc = GenomeLocParser.createGenomeLoc(obj1);
GenomeLoc hisLoc = GenomeLocParser.createGenomeLoc(obj2);
int comparison = myLoc.compareTo(hisLoc);
// if the reads have the same start position, we must give a non-zero comparison
// (because java Sets often require "consistency with equals")
if ( comparison == 0 )
comparison = obj1.getReadName().compareTo(obj2.getReadName());
return comparison;
}
});
set.addAll(locus1.getReads());
set.addAll(locus2.getReads());
return new LocusContext(loc, new ArrayList<SAMRecord>(set), null);
}
protected <M, T> T carryWalkerOverInterval(LocusWindowWalker<M, T> walker, T sum, LocusContext window) {
ReferenceIterator refSite = refIter.seekForward(window.getLocation());
StringBuffer refBases = new StringBuffer(refSite.getBaseAsString());
int locusLength = (int)(window.getLocation().getStop() - window.getLocation().getStart());
for ( int i = 0; i < locusLength; i++ ) {
refSite = refSite.next();
refBases.append(refSite.getBaseAsChar());
}
window.setReferenceContig(refSite.getCurrentContig());
String refBases = new String(sequenceFile.getSubsequenceAt(window.getContig(),window.getLocation().getStart(),window.getLocation().getStop()).getBases());
// Iterate forward to get all reference ordered data covering this interval
final RefMetaDataTracker tracker = getReferenceOrderedDataAtLocus(window.getLocation());
sum = walkAtinterval( walker, sum, window, refBases.toString(), tracker );
sum = walkAtinterval( walker, sum, window, refBases, tracker );
printProgress("intervals", window.getLocation());