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* Copyright (c) 2012 The Broad Institute
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* The above copyright notice and this permission notice shall be
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package org.broadinstitute.gatk.engine.datasources.reads;
import com.google.caliper.Param;
import com.google.caliper.SimpleBenchmark;
import htsjdk.samtools.util.SamLocusIterator;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.CloseableIterator;
import java.io.File;
import java.util.Iterator;
/**
* Created by IntelliJ IDEA.
* User: mhanna
* Date: Apr 22, 2011
* Time: 3:51:06 PM
* To change this template use File | Settings | File Templates.
*/
public class PicardBaselineBenchmark extends ReadProcessingBenchmark {
@Param
private String bamFile;
@Param
private Integer maxReads;
@Override
public String getBAMFile() { return bamFile; }
@Override
public Integer getMaxReads() { return maxReads; }
public void timeDecompressBamFile(int reps) {
for(int i = 0; i < reps; i++) {
SAMFileReader reader = new SAMFileReader(inputFile);
CloseableIterator<SAMRecord> iterator = reader.iterator();
while(iterator.hasNext())
iterator.next();
iterator.close();
reader.close();
}
}
public void timeExtractTag(int reps) {
for(int i = 0; i < reps; i++) {
SAMFileReader reader = new SAMFileReader(inputFile);
CloseableIterator<SAMRecord> iterator = reader.iterator();
while(iterator.hasNext()) {
SAMRecord read = iterator.next();
read.getAttribute("OQ");
}
iterator.close();
reader.close();
}
}
public void timeSamLocusIterator(int reps) {
for(int i = 0; i < reps; i++) {
SAMFileReader reader = new SAMFileReader(inputFile);
long loci = 0;
SamLocusIterator samLocusIterator = new SamLocusIterator(reader);
samLocusIterator.setEmitUncoveredLoci(false);
Iterator<SamLocusIterator.LocusInfo> workhorseIterator = samLocusIterator.iterator();
while(workhorseIterator.hasNext()) {
SamLocusIterator.LocusInfo locusInfo = workhorseIterator.next();
// Use the value of locusInfo to avoid optimization.
if(locusInfo != null) loci++;
}
System.out.printf("Total loci = %d%n",loci);
reader.close();
}
}
}