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remove RodBed and all it's dependencies. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3396 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-05-19 19:12:30 +00:00
parent ffb1b46166
commit 02cc1afdc8
4 changed files with 12 additions and 123 deletions
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110
java/src/org/broadinstitute/sting/gatk/refdata/RodBed.java
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@ -1,110 +0,0 @@
/*
* 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
* 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.refdata;
import java.util.*;
import java.io.IOException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import net.sf.samtools.util.CloseableIterator;
/**
* Simple bed format parser:
*
* http://genome.ucsc.edu/FAQ/FAQformat.html
*
*
* User: mdepristo
* Date: April 20, 2010
* Time: 10:47:14 AM
*/
public class RodBed extends BasicReferenceOrderedDatum {
protected GenomeLoc loc;
private List<String> fields;
// ----------------------------------------------------------------------
//
// Constructors
//
// ----------------------------------------------------------------------
public RodBed(final String name) {
super(name);
}
// ----------------------------------------------------------------------
//
// ROD accessors
//
// ----------------------------------------------------------------------
public GenomeLoc getLocation() {
return loc;
}
//
// public ArrayList<String> getHeader() {
// return header;
// }
public List<String> getFields(final Object key) {
return fields;
}
// ----------------------------------------------------------------------
//
// formatting
//
// ----------------------------------------------------------------------
public String toString() { return "BED: " + Utils.join("\t", fields); }
/**
* Used by ROD management system to set the data in this ROD associated with a line in a rod
*
* @param headerObj
* @param parts
* @return
* @throws IOException
*/
public boolean parseLine(final Object headerObj, final String[] parts) throws IOException {
if ( parts.length < 4 )
throw new StingException("BED format requires at least 3 fields: contig start and stop");
String contig = parts[0];
int start = Integer.valueOf(parts[1]) + 1; // 1 indel
int stop = Integer.valueOf(parts[2]) + 1; // 1 indel
loc = GenomeLocParser.parseGenomeLoc(contig, start, stop);
fields = Arrays.asList(parts);
// for ( int i = 0; i < parts.length; i++ ) {
// fields.add(parts[i]);
// }
return true;
}
}

3
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
View File

@ -63,8 +63,7 @@ public class RODTrackBuilder implements RMDTrackBuilder {
Types.put("PicardDbSNP", rodPicardDbSNP.class);
Types.put("HapmapVCF", HapmapVCFROD.class);
Types.put("Beagle", BeagleROD.class);
Types.put("Plink", PlinkRod.class);
Types.put("Bed", RodBed.class);
Types.put("Plink", PlinkRod.class);
}
/**

3
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
View File

@ -76,8 +76,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
public Map<String, Class> getAvailableTrackNamesAndTypes() {
Map<String, Class> classes = new HashMap<String, Class>();
for (String c : this.pluginsByName.keySet())
if (!c.contains("BED")) // ugg the collision for Bed files is a problem right now
classes.put(c,this.pluginsByName.get(c));
classes.put(c, this.pluginsByName.get(c));
return classes;
}

19
java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broad.tribble.bed.BEDFeature;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -31,7 +32,7 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
private HashMap<GenomeLoc,IntervalInfoBuilder> intervalBuffer = new HashMap<GenomeLoc,IntervalInfoBuilder>();
private HashSet<rodRefSeq> refseqBuffer = new HashSet<rodRefSeq>();
private RodBed currentTCGA = null;
private BEDFeature currentTCGA = null;
public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// three items to look up: interval_list, tcga, and refseq
@ -67,7 +68,7 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
// update the current tcga target
if ( tcgaList != null && tcgaList.size() > 0 ) {
currentTCGA = (RodBed) tcgaList.get(0);
currentTCGA = (BEDFeature) tcgaList.get(0);
}
cleanup(ref);
@ -96,13 +97,13 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
}
if ( currentTCGA != null &&
interval.overlapsP(currentTCGA.getLocation()) &&
currentTCGA.getFields(null).size() > 2 &&
! intervalBuffer.get(interval).geneNames.contains("TCGA_"+currentTCGA.getFields(null).get(3)) ) {
interval.overlapsP(GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd())) &&
!currentTCGA.getName().equals("") &&
! intervalBuffer.get(interval).geneNames.contains("TCGA_"+currentTCGA.getName()) ) {
intervalBuffer.get(interval).update("TCGA_"+currentTCGA.getFields(null).get(3).split("_f|_r")[0],
new ArrayList<GenomeLoc>(Arrays.asList(currentTCGA.getLocation())),
new ArrayList<Integer>(Arrays.asList(Integer.parseInt(currentTCGA.getFields(null).get(3).split("_f|_r")[1])-1)));
intervalBuffer.get(interval).update("TCGA_"+currentTCGA.getName().split("_f|_r")[0],
new ArrayList<GenomeLoc>(Arrays.asList(GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd()))),
new ArrayList<Integer>(Arrays.asList(Integer.parseInt(currentTCGA.getName().split("_f|_r")[1])-1)));
}
}
@ -138,7 +139,7 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
intervalBuffer.remove(interval);
}
if ( currentTCGA != null && currentTCGA.getLocation().isBefore(ref.getLocus()) ) {
if ( currentTCGA != null && GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd()).isBefore(ref.getLocus()) ) {
currentTCGA = null;
}
}