Fare thee well, oh LocusWindowTraversal.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3089 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -744,17 +744,6 @@ public class GenomeAnalysisEngine {
                     ShardStrategyFactory.SHATTER_STRATEGY.READS_EXPERIMENTAL,
                     drivingDataSource.getSequenceDictionary(),
                     SHARD_SIZE, maxIterations);
-
-        } else if (walker instanceof LocusWindowWalker) {
-            if ((intervals == null || intervals.isEmpty()) && !exclusions.contains(ValidationExclusion.TYPE.ALLOW_EMPTY_INTERVAL_LIST))
-                Utils.warnUser("walker is of type LocusWindow (which operates over intervals), but no intervals were provided." +
-                               "This may be unintentional, check your command-line arguments.");
-            shardStrategy = ShardStrategyFactory.shatter(readsDataSource,
-                    referenceDataSource,
-                    ShardStrategyFactory.SHATTER_STRATEGY.INTERVAL,
-                    drivingDataSource.getSequenceDictionary(),
-                    SHARD_SIZE,
-                    intervals, maxIterations);
         } else
             throw new StingException("Unable to support walker of type" + walker.getClass().getName());
 

java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -38,7 +38,6 @@ import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
 import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
 import java.util.*;
 import java.io.File;
@@ -107,8 +106,6 @@ public abstract class MicroScheduler {
             traversalEngine = new TraverseReads();
         } else if (walker instanceof LocusWalker) {
             traversalEngine = new TraverseLoci();
-        } else if (walker instanceof LocusWindowWalker) {
-            traversalEngine = new TraverseLocusWindows();
         } else if (walker instanceof DuplicateWalker) {
             traversalEngine = new TraverseDuplicates();
         } else if (walker instanceof ReadPairWalker) {

java/src/org/broadinstitute/sting/gatk/traversals/TraverseLocusWindows.java

@@ -1,106 +0,0 @@
-package org.broadinstitute.sting.gatk.traversals;
-
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.datasources.providers.*;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.iterators.LocusIterator;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Pair;
-
-import java.util.*;
-
-/**
- * Created by IntelliJ IDEA.
- * User: ebanks
- * Date: Apr 23, 2009
- * Time: 10:26:03 AM
- * To change this template use File | Settings | File Templates.
- */
-public class TraverseLocusWindows<M,T> extends TraversalEngine<M,T,LocusWindowWalker<M,T>,LocusShardDataProvider> {
-    /** descriptor of the type */
-    private static final String LOCUS_WINDOW_STRING = "intervals";
-
-    public T traverse( LocusWindowWalker<M,T> walker,
-                       LocusShardDataProvider dataProvider,
-                       T sum ) {
-
-        GenomeLoc interval = dataProvider.getLocus();
-
-        LocusReferenceView referenceView = new LocusReferenceView( walker, dataProvider );
-        ReferenceOrderedView referenceOrderedDataView = new ManagingReferenceOrderedView( dataProvider );
-
-        Pair<GenomeLoc, List<SAMRecord>> locus = getLocusContext(dataProvider.getLocusIterator(), interval);
-
-        // The TraverseByLocusWindow expands intervals to cover all reads in a non-standard way.
-        // TODO: Convert this approach to the standard.
-        GenomeLoc expandedInterval = locus.getFirst();
-
-        String referenceSubsequence = new String(referenceView.getReferenceBases(expandedInterval));
-
-        // Iterate forward to get all reference ordered data covering this interval
-        final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getFirst());
-
-        //
-        // Execute our contract with the walker.  Call filter, map, and reduce
-        //
-        //final boolean keepMeP = locusWindowWalker.filter(tracker, referenceSubsequence, locus);
-        //if (keepMeP) {
-        M x = walker.map(tracker, referenceSubsequence, locus.getFirst(), locus.getSecond());
-        sum = walker.reduce(x, sum);
-        //}
-
-        printProgress(LOCUS_WINDOW_STRING, locus.getFirst());
-
-        return sum;
-    }
-
-    private Pair<GenomeLoc, List<SAMRecord>> getLocusContext(LocusIterator locusIter, GenomeLoc interval) {
-        List<SAMRecord> reads = new ArrayList<SAMRecord>();
-        boolean done = false;
-        long leftmostIndex = interval.getStart(),
-                rightmostIndex = interval.getStop();
-
-        while(locusIter.hasNext() && !done) {
-            AlignmentContext alignment = locusIter.next();
-            Iterator<SAMRecord> readIter = alignment.getReads().iterator();
-
-            while (readIter.hasNext() && !done) {
-                TraversalStatistics.nRecords++;
-
-                SAMRecord read = readIter.next();
-                if(reads.contains(read)) continue;
-                reads.add(read);
-                if ( read.getAlignmentStart() < leftmostIndex )
-                    leftmostIndex = read.getAlignmentStart();
-                if ( read.getAlignmentEnd() > rightmostIndex )
-                    rightmostIndex = read.getAlignmentEnd();
-                if ( this.maximumIterations > 0 && TraversalStatistics.nRecords > this.maximumIterations) {
-                    logger.warn(String.format("Maximum number of reads encountered, terminating traversal " + TraversalStatistics.nRecords));
-                    done = true;
-                }
-            }
-        }
-
-
-        GenomeLoc window = GenomeLocParser.createGenomeLoc(interval.getContig(), leftmostIndex, rightmostIndex);
-//        AlignmentContext locus = new AlignmentContext(window, reads, null);
-//        if ( readIter.getSourceInfo().getDownsampleToCoverage() != null )
-//            locus.downsampleToCoverage(readIter.getSourceInfo().getDownsampleToCoverage());
-
-        return new Pair<GenomeLoc, List<SAMRecord>>(window, reads);
-    }
-
-    /**
-     * Temporary override of printOnTraversalDone.
-     * TODO: Add some sort of TE.getName() function once all TraversalEngines are ported.
-     * @param sum Result of the computation.
-     */
-    public void printOnTraversalDone( T sum ) {
-        printOnTraversalDone(LOCUS_WINDOW_STRING, sum );
-    }
-
-}

java/src/org/broadinstitute/sting/gatk/walkers/LocusWindowWalker.java

@@ -1,25 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers;
-
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import net.sf.samtools.SAMRecord;
-
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: ebanks
- * Date: Apr 23, 2009
- * Time: 2:52:28 PM
- * To change this template use File | Settings | File Templates.
- */
-@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
-public abstract class LocusWindowWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
-    // Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
-    public abstract MapType map(RefMetaDataTracker tracker, String ref, GenomeLoc loc, List<SAMRecord> reads);
-
-    // Given result of map function
-    public abstract ReduceType reduceInit();
-    public abstract ReduceType reduce(MapType value, ReduceType sum);
-}