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Conditional support for PerformanceTrackingQuerySource to measure Tribble / GATK bridge performance 

-- Removed DEBUG option, instead use MEASURE_TRIBBLE_QUERY_PERFORMANCE in RMDTrackerBuilder
This commit is contained in:
Mark DePristo 2011-09-01 10:41:55 -04:00
parent 2b97017871
commit ac49b8d26b
2 changed files with 21 additions and 9 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
View File

@ -26,8 +26,11 @@ 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.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureSource; import org.broad.tribble.FeatureSource;
import org.broad.tribble.iterators.CloseableTribbleIterator;
import org.broad.tribble.source.PerformanceLoggingFeatureSource;
import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator; import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
@ -47,7 +50,6 @@ import java.io.IOException;
*/ */
public class RMDTrack { public class RMDTrack {
private final static Logger logger = Logger.getLogger(RMDTrackBuilder.class); 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
@ -113,8 +115,10 @@ public class RMDTrack {
} }
public CloseableIterator<GATKFeature> query(GenomeLoc interval) throws IOException { public CloseableIterator<GATKFeature> query(GenomeLoc interval) throws IOException {
if ( DEBUG ) logger.debug("Issuing query for %s: " + interval); CloseableTribbleIterator<Feature> iter = reader.query(interval.getContig(),interval.getStart(),interval.getStop());
return new FeatureToGATKFeatureIterator(genomeLocParser, reader.query(interval.getContig(),interval.getStart(),interval.getStop()), this.getName()); if ( RMDTrackBuilder.MEASURE_TRIBBLE_QUERY_PERFORMANCE )
logger.warn("Query " + getName() + ":" + ((PerformanceLoggingFeatureSource)reader).getPerformanceLog());
return new FeatureToGATKFeatureIterator(genomeLocParser, iter, this.getName());
} }
public void close() { public void close() {

18
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
View File

@ -27,20 +27,21 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broad.tribble.*; import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureSource;
import org.broad.tribble.Tribble;
import org.broad.tribble.TribbleException;
import org.broad.tribble.index.Index; import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory; import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.source.PerformanceLoggingFeatureSource;
import org.broad.tribble.util.LittleEndianOutputStream; import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.SequenceDictionaryUtils; import org.broadinstitute.sting.utils.SequenceDictionaryUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -51,7 +52,10 @@ import org.broadinstitute.sting.utils.instrumentation.Sizeof;
import java.io.File; import java.io.File;
import java.io.FileOutputStream; import java.io.FileOutputStream;
import java.io.IOException; import java.io.IOException;
import java.util.*; import java.util.LinkedHashSet;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
@ -70,6 +74,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
* our log, which we use to capture anything from this class * our log, which we use to capture anything from this class
*/ */
private final static Logger logger = Logger.getLogger(RMDTrackBuilder.class); private final static Logger logger = Logger.getLogger(RMDTrackBuilder.class);
public final static boolean MEASURE_TRIBBLE_QUERY_PERFORMANCE = false;
// a constant we use for marking sequence dictionary entries in the Tribble index property list // a constant we use for marking sequence dictionary entries in the Tribble index property list
public static final String SequenceDictionaryPropertyPredicate = "DICT:"; public static final String SequenceDictionaryPropertyPredicate = "DICT:";
@ -214,6 +219,9 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
sequenceDictionary = getSequenceDictionaryFromProperties(index); sequenceDictionary = getSequenceDictionaryFromProperties(index);
} }
if ( MEASURE_TRIBBLE_QUERY_PERFORMANCE )
featureSource = new PerformanceLoggingFeatureSource(inputFile.getAbsolutePath(), index, createCodec(descriptor, name));
else
featureSource = new BasicFeatureSource(inputFile.getAbsolutePath(), index, createCodec(descriptor, name)); featureSource = new BasicFeatureSource(inputFile.getAbsolutePath(), index, createCodec(descriptor, name));
} }
catch (TribbleException e) { catch (TribbleException e) {