Bed ROD track support

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3225 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,107 @@
+/*
+ * Copyright (c) 2009 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, sub ject 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 ÓAS ISÓ, 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

@@ -73,6 +73,7 @@ public class RODTrackBuilder implements RMDTrackBuilder {
         Types.put("HapmapVCF", HapmapVCFROD.class);
         Types.put("Beagle", BeagleROD.class);
         Types.put("Plink", PlinkRod.class);
+        Types.put("Bed", RodBed.class);
     }
 
     /**