a start to some of the infrastructure for Tribble, including dynamic detection of new RMD; not nearly wired in or complete yet.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2855 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
bbbad79f8c
commit
33ae256186
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@ -0,0 +1,94 @@
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/*
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* Copyright (c) 2010. The Broad Institute
|
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* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.
|
||||
*/
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package org.broadinstitute.sting.gatk.refdata.tracks;
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import org.broad.tribble.FeatureReader;
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import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.StingException;
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import java.io.File;
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import java.io.IOException;
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import java.util.Iterator;
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/**
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*
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* @author aaron
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*
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* Class FeatureReaderTrack
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*
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* A feature reader track, implementing the RMDTrack for tracks that are generated out of Tribble
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*/
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public class FeatureReaderTrack extends RMDTrack implements QueryableTrack {
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// our feature reader - allows queries
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private FeatureReader reader;
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/**
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* Create a track
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*
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* @param type the type of track, used for track lookup
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* @param name the name of this specific track
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* @param file the associated file, for reference or recreating the reader
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* @param reader the feature reader to use as the underlying data source
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*/
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public FeatureReaderTrack(Class type, String name, File file, FeatureReader reader) {
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super(type, name, file);
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this.reader = reader;
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}
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/**
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* @return how to get an iterator of the underlying data. This is all a track has to support,
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* but other more advanced tracks support the query interface
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*/
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@Override
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public Iterator<GATKFeature> getIterator() {
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try {
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return new FeatureToGATKFeatureIterator(reader.iterator(),this.getName());
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} catch (IOException e) {
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throw new StingException("Unable to read from file",e);
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}
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}
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@Override
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public Iterator<GATKFeature> query(GenomeLoc interval) throws IOException {
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return new FeatureToGATKFeatureIterator(reader.query(interval.getContig(),(int)interval.getStart(),(int)interval.getStop()),this.getName());
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}
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@Override
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public Iterator<GATKFeature> query(GenomeLoc interval, boolean contained) throws IOException {
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return new FeatureToGATKFeatureIterator(reader.query(interval.getContig(),(int)interval.getStart(),(int)interval.getStop(), contained),this.getName());
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}
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@Override
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public Iterator<GATKFeature> query(String contig, int start, int stop) throws IOException {
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return new FeatureToGATKFeatureIterator(reader.query(contig,start,stop),this.getName());
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}
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@Override
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public Iterator<GATKFeature> query(String contig, int start, int stop, boolean contained) throws IOException {
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return new FeatureToGATKFeatureIterator(reader.query(contig,start,stop, contained),this.getName());
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}
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}
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@ -0,0 +1,44 @@
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/*
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* Copyright (c) 2010. The Broad Institute
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* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.
|
||||
*/
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package org.broadinstitute.sting.gatk.refdata.tracks;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.io.IOException;
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import java.util.Iterator;
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/**
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* @author aaron
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* <p/>
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* Interface QueryableTrack
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* <p/>
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* a decorator interface for tracks that are queryable
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*/
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public interface QueryableTrack {
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public Iterator<GATKFeature> query(final GenomeLoc interval) throws IOException;
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public Iterator<GATKFeature> query(final GenomeLoc interval, final boolean contained) throws IOException;
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public Iterator<GATKFeature> query(final String contig, final int start, final int stop) throws IOException;
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public Iterator<GATKFeature> query(final String contig, final int start, final int stop, final boolean contained) throws IOException;
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}
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@ -0,0 +1,88 @@
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/*
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* Copyright (c) 2010. The Broad Institute
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* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.
|
||||
*/
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package org.broadinstitute.sting.gatk.refdata.tracks;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import java.io.File;
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import java.util.Iterator;
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/**
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* @author aaron
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* <p/>
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* Class RMDTrack
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* <p/>
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* the basics of what a reference metadata track must contain.
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*/
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public abstract class RMDTrack {
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// the basics of a track:
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private final Class type; // our type
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private final String name; // the name
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private final File file; // the associated file we create the reader from
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/**
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* Create a track
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*
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* @param type the type of track, used for track lookup
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* @param name the name of this specific track
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* @param file the associated file, for reference or recreating the reader
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*/
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protected RMDTrack(Class type, String name, File file) {
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this.type = type;
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this.name = name;
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this.file = file;
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}
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public Class getType() {
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return type;
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}
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public String getName() {
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return name;
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}
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public File getFile() {
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return file;
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}
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/**
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* @return how to get an iterator of the underlying data. This is all a track has to support,
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* but other more advanced tracks support the query interface
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*/
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public abstract Iterator<GATKFeature> getIterator();
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/**
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* helper function for determining if we are the same track
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*
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* @param name the name to match
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* @param type the type to match
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*
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* @return true on a match, false if the name or type is different
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*/
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public boolean matches(String name, String type) {
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return (name.equals(this.name) && type.equals(this.type.getSimpleName()));
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}
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}
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@ -0,0 +1,45 @@
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/*
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* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.
|
||||
*/
|
||||
|
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package org.broadinstitute.sting.gatk.refdata.tracks;
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import org.broadinstitute.sting.utils.StingException;
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/**
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*
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* @author aaron
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*
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* Class RMDTrackCreationException
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*
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* if we fail for some reason to make a track, throw this exception
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*/
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public class RMDTrackCreationException extends StingException {
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public RMDTrackCreationException(String msg) {
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super(msg);
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}
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public RMDTrackCreationException(String message, Throwable throwable) {
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super(message, throwable);
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}
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}
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@ -0,0 +1,126 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.
|
||||
*/
|
||||
|
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package org.broadinstitute.sting.gatk.refdata.tracks;
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import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
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import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
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import org.broadinstitute.sting.utils.PluginManager;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.Utils;
|
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|
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import java.io.File;
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import java.util.ArrayList;
|
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import java.util.HashMap;
|
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import java.util.List;
|
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import java.util.Map;
|
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|
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|
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/**
|
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* @author aaron
|
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* <p/>
|
||||
* Class RMDTrackManager
|
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* <p/>
|
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* Find the available track builders, and create the requisite tracks from the command line.
|
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*/
|
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public class RMDTrackManager extends PluginManager<RMDTrackBuilder> {
|
||||
// the input strings we use to create RODs from
|
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List<RMDTriplet> inputs = new ArrayList<RMDTriplet>();
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|
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// create an active mapping of builder instances, and a map of the name -> class for convenience
|
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Map<String, RMDTrackBuilder> availableTracks;
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Map<String, Class> availableTrackClasses;
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|
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/** Create a new track plugin manager. */
|
||||
protected RMDTrackManager() {
|
||||
super(RMDTrackBuilder.class, "TrackBuilders", null);
|
||||
}
|
||||
|
||||
/**
|
||||
* find the associated reference meta data
|
||||
*
|
||||
* @param triplets the triplets of strings from the -B command line option
|
||||
*
|
||||
* @return a list of RMDTracks, one for each -B option
|
||||
*/
|
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public List<RMDTrack> getReferenceMetaDataSources(List<String> triplets) {
|
||||
if (availableTracks == null || availableTrackClasses == null) initialize(triplets);
|
||||
// try and make the tracks given their requests
|
||||
return createTracksRequestedTrackObjects(availableTracks, availableTrackClasses);
|
||||
}
|
||||
|
||||
/**
|
||||
* initialize our lists of tracks and builders
|
||||
* @param triplets the input to the GATK, as a list of strings passed in through the -B options
|
||||
*/
|
||||
private void initialize(List<String> triplets) {
|
||||
if (triplets.size() % 3 != 0) throw new StingException("Incorect ROD line " + Utils.join(" ", triplets));
|
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for (int x = 0; x < triplets.size(); x = x + 3) {
|
||||
inputs.add(new RMDTriplet(triplets.get(x), triplets.get(x + 1), triplets.get(x + 2)));
|
||||
}
|
||||
|
||||
// create an active mapping of builder instances, and a map of the name -> class for convenience
|
||||
availableTracks = new HashMap<String, RMDTrackBuilder>();
|
||||
availableTrackClasses = new HashMap<String, Class>();
|
||||
createBuilderObjects();
|
||||
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* create the builder objects from the retrieved list
|
||||
*/
|
||||
private void createBuilderObjects() {
|
||||
// create a track builder instance for each track builder, and find out what tracks we can make
|
||||
for (String builderName : this.pluginsByName.keySet()) {
|
||||
RMDTrackBuilder builder = this.createByName(builderName);
|
||||
for (String name : builder.getAvailableTrackNamesAndTypes().keySet()) {
|
||||
availableTracks.put(name.toUpperCase(), builder);
|
||||
availableTrackClasses.put(name.toUpperCase(), builder.getAvailableTrackNamesAndTypes().get(name));
|
||||
System.err.println("Adding track " + name.toUpperCase());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* create the requested track objects
|
||||
*
|
||||
* @param availableTracks the tracks that are available to us, associated with their builder
|
||||
* @param availableTrackClasses the classes names, with their class description
|
||||
*
|
||||
* @return a list of the tracks, one for each of the requested input tracks
|
||||
*/
|
||||
private List<RMDTrack> createTracksRequestedTrackObjects(Map<String, RMDTrackBuilder> availableTracks, Map<String, Class> availableTrackClasses) {
|
||||
// create of live instances of the tracks
|
||||
List<RMDTrack> tracks = new ArrayList<RMDTrack>();
|
||||
|
||||
// create instances of each of the requested types
|
||||
for (RMDTriplet trip : inputs) {
|
||||
RMDTrackBuilder b = availableTracks.get(trip.getType());
|
||||
if (b == null) throw new StingException("Unable to find track for " + trip.getType());
|
||||
tracks.add(b.createInstanceOfTrack(availableTrackClasses.get(trip.getType()), trip.getName(), new File(trip.getFile())));
|
||||
}
|
||||
return tracks;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.refdata.tracks;
|
||||
|
||||
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.Iterator;
|
||||
|
||||
|
||||
|
||||
/**
|
||||
*
|
||||
* @author aaron
|
||||
*
|
||||
* Class RODRMDTrack
|
||||
*
|
||||
* wrap a reference ordered data object in the new track style. This will hopefully be phased-out as we move to
|
||||
* a FeatureReader based system.
|
||||
*/
|
||||
public class RODRMDTrack extends RMDTrack {
|
||||
|
||||
// our ROD
|
||||
private ReferenceOrderedData data;
|
||||
|
||||
/**
|
||||
* Create a track
|
||||
*
|
||||
* @param type the type of track, used for track lookup
|
||||
* @param name the name of this specific track
|
||||
* @param file the associated file, for reference or recreating the reader
|
||||
* @param data the ROD to use as the underlying data source for this track
|
||||
*/
|
||||
public RODRMDTrack(Class type, String name, File file, ReferenceOrderedData data) {
|
||||
super(type, name, file);
|
||||
this.data = data;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return how to get an iterator of the underlying data. This is all a track has to support,
|
||||
* but other more advanced tracks support the query interface
|
||||
*/
|
||||
@Override
|
||||
public Iterator<GATKFeature> getIterator() {
|
||||
return data.iterator();
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,58 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.refdata.tracks.builders;
|
||||
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.Map;
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* @author aaron
|
||||
* <p/>
|
||||
* Interface RMDTrackBuilder
|
||||
* <p/>
|
||||
* The basic interface for finding and parsing RMDTracks. Track builders present an interface that allows
|
||||
* the track manager to find and create tracks of the specified type.
|
||||
*/
|
||||
public interface RMDTrackBuilder {
|
||||
|
||||
/** @return a list of all available tracks types we currently have access to create */
|
||||
public Map<String, Class> getAvailableTrackNamesAndTypes();
|
||||
|
||||
/**
|
||||
* create a RMDTrack of the specified type
|
||||
*
|
||||
* @param targetClass the target class of track
|
||||
* @param name what to call the track
|
||||
* @param inputFile the input file
|
||||
*
|
||||
* @return an instance of the track
|
||||
* @throws RMDTrackCreationException if we don't know of the target class or we couldn't create it
|
||||
*/
|
||||
public RMDTrack createInstanceOfTrack(Class targetClass, String name, File inputFile) throws RMDTrackCreationException;
|
||||
}
|
||||
|
|
@ -0,0 +1,134 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.refdata.tracks.builders;
|
||||
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broad.tribble.FeatureCodec;
|
||||
import org.broad.tribble.FeatureReader;
|
||||
import org.broad.tribble.index.LinearIndex;
|
||||
import org.broad.tribble.index.LinearIndexCreator;
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureReaderTrack;
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
|
||||
import org.broadinstitute.sting.utils.PluginManager;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.IOException;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
|
||||
/**
|
||||
*
|
||||
* @author aaron
|
||||
*
|
||||
* Class TribbleRMDTrackBuilder
|
||||
*
|
||||
* This class keeps track of the available codecs, and knows how to put together a track of
|
||||
* that gets iterators from the FeatureReader using Tribble.
|
||||
*/
|
||||
public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implements RMDTrackBuilder {
|
||||
|
||||
// the linear index extension
|
||||
private static final String linearIndexExtension = ".idx";
|
||||
|
||||
/** Create a new plugin manager. */
|
||||
public TribbleRMDTrackBuilder() {
|
||||
super(FeatureCodec.class, "Codecs", "Codec");
|
||||
}
|
||||
|
||||
/** @return a list of all available tracks we currently have access to create */
|
||||
@Override
|
||||
public Map<String, Class> getAvailableTrackNamesAndTypes() {
|
||||
Map<String, Class> classes = new HashMap<String, Class>();
|
||||
for (String c : this.pluginsByName.keySet())
|
||||
classes.put(c,this.pluginsByName.get(c));
|
||||
return classes;
|
||||
}
|
||||
|
||||
/**
|
||||
* create a RMDTrack of the specified type
|
||||
*
|
||||
* @param targetClass the target class of track
|
||||
* @param name what to call the track
|
||||
* @param inputFile the input file
|
||||
*
|
||||
* @return an instance of the track
|
||||
* @throws RMDTrackCreationException
|
||||
* if we don't know of the target class or we couldn't create it
|
||||
*/
|
||||
@Override
|
||||
public RMDTrack createInstanceOfTrack(Class targetClass, String name, File inputFile) throws RMDTrackCreationException {
|
||||
// make a feature reader
|
||||
FeatureReader reader;
|
||||
try {
|
||||
FeatureCodec codec = this.createByType(targetClass);
|
||||
|
||||
// check to see if the input file has an index
|
||||
if (!(new File(inputFile.getAbsolutePath() + linearIndexExtension).canRead())) {
|
||||
LinearIndex index = createIndex(inputFile, codec);
|
||||
reader = new FeatureReader(inputFile,index, codec);
|
||||
}
|
||||
else {
|
||||
reader = new FeatureReader(inputFile,codec);
|
||||
}
|
||||
} catch (FileNotFoundException e) {
|
||||
throw new StingException("Unable to create reader with file " + inputFile, e);
|
||||
} catch (IOException e) {
|
||||
throw new StingException("Unable to make the index file for " + inputFile, e);
|
||||
}
|
||||
// return a feature reader track
|
||||
return new FeatureReaderTrack(targetClass, name, inputFile, reader);
|
||||
}
|
||||
|
||||
/**
|
||||
* create an index for the input file
|
||||
* @param inputFile the input file
|
||||
* @param codec the codec to use
|
||||
* @return a linear index for the specified type
|
||||
* @throws IOException if we cannot write the index file
|
||||
*/
|
||||
private LinearIndex createIndex(File inputFile, FeatureCodec codec) throws IOException {
|
||||
LinearIndexCreator create = new LinearIndexCreator(inputFile, codec);
|
||||
return create.createIndex();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* a fake Tribble track, used to test out the Tribble interface and feature codec detection
|
||||
*/
|
||||
class FakeTribbleTrack implements FeatureCodec {
|
||||
|
||||
@Override
|
||||
public Feature decode(String s) {
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int headerLineCount(File file) {
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,62 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.refdata.utils;
|
||||
|
||||
import org.broad.tribble.Feature;
|
||||
|
||||
import java.util.Iterator;
|
||||
|
||||
|
||||
/**
|
||||
*
|
||||
* @author aaron
|
||||
*
|
||||
* Class FeatureToGATKFeatureIterator
|
||||
*
|
||||
* a wrapper on Tribble feature iterators so that they produce GATKFeatures (which produce GenomeLocs)
|
||||
*/
|
||||
public class FeatureToGATKFeatureIterator implements Iterator<GATKFeature> {
|
||||
private final Iterator<Feature> iterator;
|
||||
private final String name;
|
||||
|
||||
public FeatureToGATKFeatureIterator(Iterator<Feature> iter, String name) {
|
||||
this.name = name;
|
||||
this.iterator = iter;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean hasNext() {
|
||||
return iterator.hasNext();
|
||||
}
|
||||
|
||||
@Override
|
||||
public GATKFeature next() {
|
||||
return new TribbleGATKFeature(iterator.next(),name);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void remove() {
|
||||
throw new UnsupportedOperationException("Why does Iterator have this method? We always throw an exception here");
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,139 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.refdata.utils;
|
||||
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||
|
||||
|
||||
/**
|
||||
*
|
||||
* @author aaron
|
||||
*
|
||||
* Class GATKFeature
|
||||
*
|
||||
* This wraps a Tribble feature or a RODatum so that both present the same interface: a genome loc for position and a
|
||||
* way of retrieving the track name.
|
||||
*/
|
||||
public abstract class GATKFeature implements Feature {
|
||||
|
||||
public GATKFeature(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
private String name;
|
||||
|
||||
protected void setName(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public abstract GenomeLoc getLocation();
|
||||
|
||||
public abstract Object getUnderlyingObject();
|
||||
}
|
||||
|
||||
/**
|
||||
* wrapping a Tribble feature in a GATK friendly interface
|
||||
*/
|
||||
class TribbleGATKFeature extends GATKFeature {
|
||||
private final Feature feature;
|
||||
|
||||
public TribbleGATKFeature(Feature f, String name) {
|
||||
super(name);
|
||||
feature = f;
|
||||
}
|
||||
public GenomeLoc getLocation() {
|
||||
return GenomeLocParser.createGenomeLoc(feature.getChr(), feature.getStart(), feature.getEnd());
|
||||
}
|
||||
|
||||
/** Return the features reference sequence name, e.g chromosome or contig */
|
||||
@Override
|
||||
public String getChr() {
|
||||
return feature.getChr();
|
||||
}
|
||||
|
||||
/** Return the start position in 1-based coordinates (first base is 1) */
|
||||
@Override
|
||||
public int getStart() {
|
||||
return feature.getStart();
|
||||
}
|
||||
|
||||
/**
|
||||
* Return the end position following 1-based fully closed conventions. The length of a feature is
|
||||
* end - start + 1;
|
||||
*/
|
||||
@Override
|
||||
public int getEnd() {
|
||||
return feature.getEnd();
|
||||
}
|
||||
|
||||
public Object getUnderlyingObject() {
|
||||
return feature;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* wrapping a old style rod into the new GATK feature style
|
||||
*/
|
||||
class RODGATKFeature extends GATKFeature {
|
||||
|
||||
// our data
|
||||
private ReferenceOrderedDatum datum;
|
||||
|
||||
public RODGATKFeature(ReferenceOrderedDatum datum) {
|
||||
super(datum.getName());
|
||||
this.datum = datum;
|
||||
}
|
||||
|
||||
@Override
|
||||
public GenomeLoc getLocation() {
|
||||
return datum.getLocation();
|
||||
}
|
||||
|
||||
@Override
|
||||
public Object getUnderlyingObject() {
|
||||
return datum;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getChr() {
|
||||
return datum.getLocation().getContig();
|
||||
}
|
||||
|
||||
@Override
|
||||
public int getStart() {
|
||||
return (int)datum.getLocation().getStart();
|
||||
}
|
||||
|
||||
@Override
|
||||
public int getEnd() {
|
||||
return (int)datum.getLocation().getStop();
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.refdata.utils;
|
||||
|
||||
|
||||
/** a helper class to manage our triplets of data for the -B command line option (name, type, file) */
|
||||
public class RMDTriplet {
|
||||
private String name;
|
||||
private String type;
|
||||
private String file;
|
||||
|
||||
public RMDTriplet(String name, String type, String file) {
|
||||
this.name = name;
|
||||
this.type = type;
|
||||
this.file = file;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
|
||||
public String getFile() {
|
||||
return file;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,8 +1,8 @@
|
|||
package org.broadinstitute.sting.utils;
|
||||
|
||||
import java.util.Map;
|
||||
import java.util.List;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
/**
|
||||
* Manage plugins and plugin configuration.
|
||||
|
|
@ -50,7 +50,7 @@ public abstract class PluginManager<PluginType> {
|
|||
|
||||
|
||||
/**
|
||||
* Gets a plugin with the given name, or null if no plugin exists.
|
||||
* Gets a plugin with the given name
|
||||
*
|
||||
* @param pluginName Name of the plugin to retrieve.
|
||||
* @return The plugin object if found; null otherwise.
|
||||
|
|
@ -70,7 +70,23 @@ public abstract class PluginManager<PluginType> {
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* create a plugin with the given type
|
||||
*
|
||||
* @param pluginType type of the plugin to create.
|
||||
* @return The plugin object if created; null otherwise.
|
||||
*/
|
||||
public PluginType createByType(Class pluginType) {
|
||||
try {
|
||||
return ((Class<? extends PluginType>) pluginType).newInstance();
|
||||
}
|
||||
catch( InstantiationException ex ) {
|
||||
throw new StingException(String.format("Unable to instantiate %s",pluginCategory), ex);
|
||||
}
|
||||
catch( IllegalAccessException ex ) {
|
||||
throw new StingException(String.format("Unable to access %s",pluginCategory), ex);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Create the list of available plugins and add them to the database.
|
||||
|
|
|
|||
|
|
@ -0,0 +1,98 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.refdata.tracks;
|
||||
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
import org.junit.Assert;
|
||||
import org.junit.Before;
|
||||
import org.junit.Test;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* class RMDTrackManagerTest
|
||||
* tests out the ability of the RMDTrackManager to correctly create RMDtracks based on the requested types.
|
||||
*/
|
||||
public class RMDTrackManagerTest extends BaseTest {
|
||||
List<String> triplets;
|
||||
List<RMDTrack> tracks;
|
||||
|
||||
@Before
|
||||
public void setup() {
|
||||
RMDTrackManager manager = new RMDTrackManager();
|
||||
triplets = new ArrayList<String>();
|
||||
|
||||
// add our db snp data
|
||||
triplets.add("MyDbSNP");
|
||||
triplets.add("DBSNP");
|
||||
triplets.add("testdata/small.dbsnp.rod");
|
||||
tracks = manager.getReferenceMetaDataSources(triplets);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBuilderQuery() {
|
||||
|
||||
|
||||
for (RMDTrack t : tracks) {
|
||||
|
||||
System.err.println("name = " + t.getName() + " type = " + t.getType().getSimpleName() + " file = " + t.getFile());
|
||||
int count = 0;
|
||||
Iterator<GATKFeature> fIter;
|
||||
try {
|
||||
fIter = ((FeatureReaderTrack) t).query("1", 1, 5000);
|
||||
} catch (IOException e) {
|
||||
throw new StingException("blah I/O exception");
|
||||
}
|
||||
while (fIter.hasNext()) {
|
||||
fIter.next();
|
||||
count++;
|
||||
}
|
||||
Assert.assertEquals(100, count);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBuilderIterator() {
|
||||
for (RMDTrack t : tracks) {
|
||||
|
||||
System.err.println("name = " + t.getName() + " type = " + t.getType().getSimpleName() + " file = " + t.getFile());
|
||||
int count = 0;
|
||||
Iterator<GATKFeature> fIter = null;
|
||||
fIter = t.getIterator();
|
||||
while (fIter.hasNext()) {
|
||||
fIter.next();
|
||||
count++;
|
||||
}
|
||||
Assert.assertEquals(100, count);
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
/*
|
||||
* Copyright (c) 2010. The Broad Institute
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* Þles (the ÓSoftwareÓ), 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.refdata.tracks.builders;
|
||||
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.junit.Before;
|
||||
import org.junit.Test;
|
||||
|
||||
import java.util.Map;
|
||||
|
||||
|
||||
/**
|
||||
*
|
||||
* @author aaron
|
||||
*
|
||||
* Class TribbleRMDTrackBuilderTest
|
||||
*
|
||||
* Testing out the builder for tribble Tracks (not really a functional test right now)
|
||||
*/
|
||||
public class TribbleRMDTrackBuilderTest extends BaseTest {
|
||||
private TribbleRMDTrackBuilder builder;
|
||||
|
||||
@Before
|
||||
public void setup() {
|
||||
builder = new TribbleRMDTrackBuilder();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBuilder() {
|
||||
Map<String,Class> classes = builder.getAvailableTrackNamesAndTypes();
|
||||
for (String c: classes.keySet()) {
|
||||
System.err.println("class = " + c);
|
||||
}
|
||||
//Assert.fail("Fail");
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue