122 lines
4.8 KiB
Java
122 lines
4.8 KiB
Java
package org.broadinstitute.sting.gatk.traversals;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.gatk.LocusContext;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.FastaSequenceFile2;
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import java.util.List;
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import java.util.Arrays;
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import java.util.ArrayList;
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import java.util.LinkedList;
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import java.io.File;
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import net.sf.samtools.SAMRecord;
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/**
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* Created by IntelliJ IDEA.
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* User: mdepristo
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* Date: Mar 27, 2009
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* Time: 10:26:03 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class TraverseByReads extends TraversalEngine {
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public TraverseByReads(File reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
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super(reads, ref, rods);
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}
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public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
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if ( walker instanceof ReadWalker ) {
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Walker x = walker;
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ReadWalker<?, ?> readWalker = (ReadWalker<?, ?>)x;
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return (T)this.traverseByRead(readWalker, locations);
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} else {
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throw new IllegalArgumentException("Walker isn't a read walker!");
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}
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}
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/**
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* Traverse by read -- the key driver of linearly ordered traversal of reads. Provides a single read to
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* the walker object, in coordinate order. Supports all of the
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* interaction contract implied by the read walker
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* sor
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*
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* @param walker A read walker object
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* @param <M> MapType -- the result of calling map() on walker
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* @param <> ReduceType -- the result of calling reduce() on the walker
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* @return 0 on success
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*/
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public <M, T> Object traverseByRead(ReadWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
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samReadIter = initializeReads();
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if ( refFileName != null && !locations.isEmpty() )
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GenomeLoc.setupRefContigOrdering(new FastaSequenceFile2(refFileName));
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if (refFileName == null && !walker.requiresOrderedReads() && verifyingSamReadIter != null) {
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logger.warn(String.format("STATUS: No reference file provided and unordered reads are tolerated, enabling out of order read processing."));
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if (verifyingSamReadIter != null)
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verifyingSamReadIter.setCheckOrderP(false);
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}
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verifySortOrder(refFileName != null || walker.requiresOrderedReads());
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// Initialize the walker
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walker.initialize();
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// Initialize the sum
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T sum = walker.reduceInit();
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List<Integer> offsets = Arrays.asList(0); // Offset of a single read is always 0
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boolean done = false;
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// copy the locations here in case we ever want to use the full list again later and so that we can remove efficiently
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LinkedList notYetTraversedLocations = new LinkedList(locations);
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while (samReadIter.hasNext() && !done) {
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TraversalStatistics.nRecords++;
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// get the next read
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final SAMRecord read = samReadIter.next();
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final List<SAMRecord> reads = Arrays.asList(read);
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GenomeLoc loc = GenomeLoc.genomicLocationOf(read);
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// Jump forward in the reference to this locus location
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LocusContext locus = new LocusContext(loc, reads, offsets);
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if (!loc.isUnmapped() && refIter != null) {
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final ReferenceIterator refSite = refIter.seekForward(loc);
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locus.setReferenceContig(refSite.getCurrentContig());
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}
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GenomeLoc.removePastLocs(loc, notYetTraversedLocations);
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if (GenomeLoc.overlapswithSortedLocsP(loc, notYetTraversedLocations, locations.isEmpty())) {
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//
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// execute the walker contact
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//
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final boolean keepMeP = walker.filter(locus, read);
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if (keepMeP) {
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M x = walker.map(locus, read);
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sum = walker.reduce(x, sum);
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}
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if (this.maxReads > 0 && TraversalStatistics.nRecords > this.maxReads) {
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logger.warn(String.format(("Maximum number of reads encountered, terminating traversal " + TraversalStatistics.nRecords)));
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done = true;
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}
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}
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printProgress("reads", loc);
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if (GenomeLoc.pastFinalLocation(loc, locations))
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done = true;
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//System.out.printf("Done? %b%n", done);
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}
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printOnTraversalDone("reads", sum);
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walker.onTraversalDone(sum);
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return sum;
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}
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}
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