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

java/src/org/broadinstitute/sting/gatk/refdata/RodBed.java

@@ -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;
-    }
-}

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("Plink", PlinkRod.class);        
-        Types.put("Bed", RodBed.class);
     }
 
     /**

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

@@ -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;
     }
 

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<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()) &&
+                 interval.overlapsP(GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd())) &&
-                 currentTCGA.getFields(null).size() > 2 &&
+                 !currentTCGA.getName().equals("") &&
-                 ! intervalBuffer.get(interval).geneNames.contains("TCGA_"+currentTCGA.getFields(null).get(3)) ) {
+                 ! intervalBuffer.get(interval).geneNames.contains("TCGA_"+currentTCGA.getName()) ) {
 
-                intervalBuffer.get(interval).update("TCGA_"+currentTCGA.getFields(null).get(3).split("_f|_r")[0],
+                intervalBuffer.get(interval).update("TCGA_"+currentTCGA.getName().split("_f|_r")[0],
-                        new ArrayList<GenomeLoc>(Arrays.asList(currentTCGA.getLocation())),
+                        new ArrayList<GenomeLoc>(Arrays.asList(GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd()))),
-                        new ArrayList<Integer>(Arrays.asList(Integer.parseInt(currentTCGA.getFields(null).get(3).split("_f|_r")[1])-1)));
+                        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;
         }
     }