From a5c65fc133db34228acd4e5b8cb0ba1c9a43f037 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 28 Aug 2011 18:54:49 -0400
Subject: [PATCH] Debugging information to print out the Query tracks

---
 .../sting/gatk/refdata/tracks/RMDTrack.java   | 20 +++++--------------
 1 file changed, 5 insertions(+), 15 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
index ba1ca674e..a97f3211c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
@@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.util.CloseableIterator;
+import org.apache.log4j.Logger;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.FeatureSource;
 import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
@@ -45,10 +46,11 @@ import java.io.IOException;
  *         the basics of what a reference metadata track must contain.
  */
 public class RMDTrack {
+    private final static Logger logger = Logger.getLogger(RMDTrackBuilder.class);
+    private final static boolean DEBUG = false;
 
     // the basics of a track:
     private final Class type;           // our type
-    private final Class recordType;     // the underlying records that are produced by this track
     private final String name;          // the name
     private final File file;            // the associated file we create the reader from
 
@@ -90,7 +92,6 @@ public class RMDTrack {
      */
     public RMDTrack(Class type, String name, File file, FeatureSource reader, SAMSequenceDictionary dict, GenomeLocParser genomeLocParser, FeatureCodec codec) {
         this.type = type;
-        this.recordType = codec.getFeatureType();
         this.name = name;
         this.file = file;
         this.reader = reader;
@@ -112,19 +113,8 @@ public class RMDTrack {
     }
 
     public CloseableIterator<GATKFeature> query(GenomeLoc interval) throws IOException {
-        return new FeatureToGATKFeatureIterator(genomeLocParser,reader.query(interval.getContig(),interval.getStart(),interval.getStop()),this.getName());
-    }
-
-    public CloseableIterator<GATKFeature> query(GenomeLoc interval, boolean contained) throws IOException {
-        return new FeatureToGATKFeatureIterator(genomeLocParser,reader.query(interval.getContig(),interval.getStart(),interval.getStop()),this.getName());
-    }
-
-    public CloseableIterator<GATKFeature> query(String contig, int start, int stop) throws IOException {
-        return new FeatureToGATKFeatureIterator(genomeLocParser,reader.query(contig,start,stop),this.getName());
-    }
-
-    public CloseableIterator<GATKFeature> query(String contig, int start, int stop, boolean contained) throws IOException {
-        return new FeatureToGATKFeatureIterator(genomeLocParser,reader.query(contig,start,stop),this.getName());
+        if ( DEBUG ) logger.debug("Issuing query for %s: " + interval);
+        return new FeatureToGATKFeatureIterator(genomeLocParser, reader.query(interval.getContig(),interval.getStart(),interval.getStop()), this.getName());
     }
 
     public void close() {