diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodBed.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodBed.java deleted file mode 100755 index 9874d8ca9..000000000 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RodBed.java +++ /dev/null @@ -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 fields; - - // ---------------------------------------------------------------------- - // - // Constructors - // - // ---------------------------------------------------------------------- - public RodBed(final String name) { - super(name); - } - - - // ---------------------------------------------------------------------- - // - // ROD accessors - // - // ---------------------------------------------------------------------- - public GenomeLoc getLocation() { - return loc; - } -// -// public ArrayList getHeader() { -// return header; -// } - - public List 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; - } -} diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java index 004bee39d..bfb18ed1c 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java @@ -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); } /** diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java index b9edd742b..344a5fa2e 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java @@ -76,8 +76,7 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen public Map getAvailableTrackNamesAndTypes() { Map classes = new HashMap(); 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; } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java index aa0b17e84..43ee6d215 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java @@ -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 { private HashMap intervalBuffer = new HashMap(); private HashSet refseqBuffer = new HashSet(); - 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 { // 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 { } 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(Arrays.asList(currentTCGA.getLocation())), - new ArrayList(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(Arrays.asList(GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd()))), + new ArrayList(Arrays.asList(Integer.parseInt(currentTCGA.getName().split("_f|_r")[1])-1))); } } @@ -138,7 +139,7 @@ public class DesignFileGeneratorWalker extends RodWalker { 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; } }