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Refactor LIBS into utils.locusiterator before refactoring

This commit is contained in:
Mark DePristo 2013-01-05 13:06:47 -05:00
parent 9ed922d562
commit b2990497e2
10 changed files with 69 additions and 66 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
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@ -29,7 +29,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.utils.locusiterator.LocusIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;

2
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
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@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.utils.locusiterator.LocusIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;

6
public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
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@ -29,9 +29,9 @@ import net.sf.picard.util.PeekableIterator;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.iterators.LegacyLocusIteratorByState;
import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
import org.broadinstitute.sting.utils.locusiterator.LegacyLocusIteratorByState;
import org.broadinstitute.sting.utils.locusiterator.LocusIterator;
import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;

56
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
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@ -1,56 +0,0 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.iterators;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import java.util.Iterator;
/**
* Iterator that traverses a SAM File, accumulating information on a per-locus basis
*/
public abstract class LocusIterator implements Iterable<AlignmentContext>, CloseableIterator<AlignmentContext> {
// -----------------------------------------------------------------------------------------------------------------
//
// constructors and other basic operations
//
// -----------------------------------------------------------------------------------------------------------------
public Iterator<AlignmentContext> iterator() {
return this;
}
public void close() {
//this.it.close();
}
public abstract boolean hasNext();
public abstract AlignmentContext next();
public void remove() {
throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
}
}

2
public/java/src/org/broadinstitute/sting/gatk/iterators/LegacyLocusIteratorByState.java → public/java/src/org/broadinstitute/sting/utils/locusiterator/LegacyLocusIteratorByState.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.iterators;
package org.broadinstitute.sting.utils.locusiterator;
import net.sf.picard.util.PeekableIterator;
import net.sf.samtools.Cigar;

31
public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java 100644
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@ -0,0 +1,31 @@
package org.broadinstitute.sting.utils.locusiterator;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import java.util.Iterator;
/**
* Iterator that traverses a SAM File, accumulating information on a per-locus basis
*/
public abstract class LocusIterator implements Iterable<AlignmentContext>, CloseableIterator<AlignmentContext> {
// -----------------------------------------------------------------------------------------------------------------
//
// constructors and other basic operations
//
// -----------------------------------------------------------------------------------------------------------------
public Iterator<AlignmentContext> iterator() {
return this;
}
public void close() {
//this.it.close();
}
public abstract boolean hasNext();
public abstract AlignmentContext next();
public void remove() {
throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
}
}

2
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java → public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.iterators;
package org.broadinstitute.sting.utils.locusiterator;
import net.sf.picard.util.PeekableIterator;
import net.sf.samtools.Cigar;

2
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
View File

@ -36,7 +36,7 @@ import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
import org.broadinstitute.sting.gatk.iterators.LegacyLocusIteratorByState;
import org.broadinstitute.sting.utils.locusiterator.LegacyLocusIteratorByState;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
import org.broadinstitute.sting.utils.GenomeLocParser;

28
public/java/test/org/broadinstitute/sting/gatk/iterators/LegacyLocusIteratorByStateUnitTest.java → public/java/test/org/broadinstitute/sting/utils/locusiterator/LegacyLocusIteratorByStateUnitTest.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.iterators;
package org.broadinstitute.sting.utils.locusiterator;
import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator;
@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
@ -49,6 +50,31 @@ import java.util.Collections;
import java.util.Iterator;
import java.util.List;
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* testing of the LEGACY version of LocusIteratorByState
*/

4
public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java → public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.iterators;
package org.broadinstitute.sting.utils.locusiterator;
import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator;
@ -34,9 +34,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;