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Renamed traversal by "interval" to "locusWindow" 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@537 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-04-26 02:26:08 +00:00
parent 9a299c11d3
commit 0c76a70313
4 changed files with 15 additions and 15 deletions
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6
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -15,7 +15,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.traversals.*; import org.broadinstitute.sting.gatk.traversals.*;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.IntervalWalker; import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
@ -278,8 +278,8 @@ public class GenomeAnalysisTK extends CommandLineProgram {
else else
this.engine = new TraverseByLoci(INPUT_FILES, REF_FILE_ARG, rods); this.engine = new TraverseByLoci(INPUT_FILES, REF_FILE_ARG, rods);
} }
} else if ( my_walker instanceof IntervalWalker ) { } else if ( my_walker instanceof LocusWindowWalker ) {
this.engine = new TraverseByIntervals(INPUT_FILES, REF_FILE_ARG, rods); this.engine = new TraverseByLocusWindows(INPUT_FILES, REF_FILE_ARG, rods);
} else { } else {
// we're a read walker // we're a read walker
this.engine = new TraverseByReads(INPUT_FILES, REF_FILE_ARG, rods); this.engine = new TraverseByReads(INPUT_FILES, REF_FILE_ARG, rods);

18
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByIntervals.java → java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.traversals; package org.broadinstitute.sting.gatk.traversals;
import org.broadinstitute.sting.gatk.walkers.IntervalWalker; import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
@ -26,16 +26,16 @@ import edu.mit.broad.picard.filter.FilteringIterator;
* Time: 10:26:03 AM * Time: 10:26:03 AM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public class TraverseByIntervals extends TraversalEngine { public class TraverseByLocusWindows extends TraversalEngine {
public TraverseByIntervals(List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) { public TraverseByLocusWindows(List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
super(reads, ref, rods); super(reads, ref, rods);
} }
public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) { public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
if ( walker instanceof IntervalWalker ) { if ( walker instanceof LocusWindowWalker ) {
IntervalWalker<M, T> intervalWalker = (IntervalWalker<M, T>)walker; LocusWindowWalker<M, T> locusWindowWalker = (LocusWindowWalker<M, T>)walker;
T sum = traverseByIntervals(intervalWalker, locations); T sum = traverseByIntervals(locusWindowWalker, locations);
return sum; return sum;
} else { } else {
throw new IllegalArgumentException("Walker isn't an interval walker!"); throw new IllegalArgumentException("Walker isn't an interval walker!");
@ -52,7 +52,7 @@ public class TraverseByIntervals extends TraversalEngine {
* @param <T> ReduceType -- the result of calling reduce() on the walker * @param <T> ReduceType -- the result of calling reduce() on the walker
* @return 0 on success * @return 0 on success
*/ */
protected <M, T> T traverseByIntervals(IntervalWalker<M, T> walker, ArrayList<GenomeLoc> locations) { protected <M, T> T traverseByIntervals(LocusWindowWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
logger.debug("Entering traverseByIntervals"); logger.debug("Entering traverseByIntervals");
if(readsFiles.size() > 1) if(readsFiles.size() > 1)
@ -90,7 +90,7 @@ public class TraverseByIntervals extends TraversalEngine {
return sum; return sum;
} }
protected <M, T> T carryWalkerOverInterval(IntervalWalker<M, T> walker, Iterator<SAMRecord> readIter, T sum, GenomeLoc interval ) { protected <M, T> T carryWalkerOverInterval(LocusWindowWalker<M, T> walker, Iterator<SAMRecord> readIter, T sum, GenomeLoc interval ) {
logger.debug(String.format("TraverseByIntervals.carryWalkerOverInterval Genomic interval is %s", interval)); logger.debug(String.format("TraverseByIntervals.carryWalkerOverInterval Genomic interval is %s", interval));
// prepare the read filtering read iterator and provide it to a new interval iterator // prepare the read filtering read iterator and provide it to a new interval iterator
@ -129,7 +129,7 @@ public class TraverseByIntervals extends TraversalEngine {
return sum; return sum;
} }
protected <M, T> T walkAtinterval( final IntervalWalker<M, T> walker, protected <M, T> T walkAtinterval( final LocusWindowWalker<M, T> walker,
T sum, T sum,
final LocusContext locus, final LocusContext locus,
final ReferenceIterator refSite, final ReferenceIterator refSite,

2
java/src/org/broadinstitute/sting/gatk/walkers/IntervalWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/LocusWindowWalker.java
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@ -10,7 +10,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
* Time: 2:52:28 PM * Time: 2:52:28 PM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public abstract class IntervalWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> { public abstract class LocusWindowWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
// Do we actually want to operate on the context? // Do we actually want to operate on the context?
public boolean filter(RefMetaDataTracker tracker, String ref, LocusContext context) { public boolean filter(RefMetaDataTracker tracker, String ref, LocusContext context) {
return true; // We are keeping all the reads return true; // We are keeping all the reads

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
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@ -2,7 +2,7 @@
package org.broadinstitute.sting.playground.gatk.walkers; package org.broadinstitute.sting.playground.gatk.walkers;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.IntervalWalker; import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName; import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -10,7 +10,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
import net.sf.samtools.*; import net.sf.samtools.*;
@WalkerName("IntervalCleaner") @WalkerName("IntervalCleaner")
public class IntervalCleanerWalker extends IntervalWalker<Integer, Integer> { public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer> {
@Argument(fullName="maxReadLength", shortName="maxRead", required=false, defaultValue="-1") @Argument(fullName="maxReadLength", shortName="maxRead", required=false, defaultValue="-1")
public int maxReadLength; public int maxReadLength;