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Debugging information to print out the Query tracks

This commit is contained in:
Mark DePristo 2011-08-28 18:54:49 -04:00
parent d1b2b4ece9
commit a5c65fc133
1 changed files with 5 additions and 15 deletions
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20
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
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@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import org.apache.log4j.Logger;
import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureSource; import org.broad.tribble.FeatureSource;
import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator; 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. * the basics of what a reference metadata track must contain.
*/ */
public class RMDTrack { public class RMDTrack {
private final static Logger logger = Logger.getLogger(RMDTrackBuilder.class);
private final static boolean DEBUG = false;
// the basics of a track: // the basics of a track:
private final Class type; // our type 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 String name; // the name
private final File file; // the associated file we create the reader from 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) { public RMDTrack(Class type, String name, File file, FeatureSource reader, SAMSequenceDictionary dict, GenomeLocParser genomeLocParser, FeatureCodec codec) {
this.type = type; this.type = type;
this.recordType = codec.getFeatureType();
this.name = name; this.name = name;
this.file = file; this.file = file;
this.reader = reader; this.reader = reader;
@ -112,19 +113,8 @@ public class RMDTrack {
} }
public CloseableIterator<GATKFeature> query(GenomeLoc interval) throws IOException { public CloseableIterator<GATKFeature> query(GenomeLoc interval) throws IOException {
return new FeatureToGATKFeatureIterator(genomeLocParser,reader.query(interval.getContig(),interval.getStart(),interval.getStop()),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 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());
} }
public void close() { public void close() {