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removed the test cases from the bottom of this file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@556 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-04-28 21:50:22 +00:00
parent 6b02248298
commit b836761104
1 changed files with 0 additions and 115 deletions
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115
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -1,12 +1,9 @@
package org.broadinstitute.sting.gatk;
import edu.mit.broad.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMFileReader.ValidationStringency;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.RuntimeIOException;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.log4j.Logger;
@ -20,7 +17,6 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import java.io.File;
import java.io.FileNotFoundException;
@ -375,117 +371,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
}
}
/**
* An inappropriately placed validation and performance testing routine for jumping
* around in the fasta sequence file.
* @param refFileName
*/
private static void testNewReferenceFeatures(final File refFileName) {
final FastaSequenceFile2 refFile = new FastaSequenceFile2(refFileName);
GenomeLoc.setupRefContigOrdering(refFile);
List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary().getSequences();
/*
for ( SAMSequenceRecord refContig: refContigs ) {
System.out.printf(" Traversing from chr1 to %s would require jumping %d bytes%n",
refContig.getSequenceName(), refFile.getDistanceBetweenContigs("chr1", refContig.getSequenceName()));
}
*/
String lastContig = null;
List<Double> timings = new ArrayList<Double>();
for ( SAMSequenceRecord startContig : refFile.getSequenceDictionary().getSequences() ) {
final String startContigName = startContig.getSequenceName();
for ( SAMSequenceRecord targetContig : refFile.getSequenceDictionary().getSequences() ) {
refFile.seekToContig(startContigName, true);
logger.info(String.format("Seeking: current=%s, target=%s%n", startContigName, targetContig.getSequenceName()));
long lastTime = System.currentTimeMillis();
final boolean success = refFile.seekToContig(targetContig.getSequenceName(), true);
long curTime = System.currentTimeMillis();
final double elapsed = (curTime - lastTime) / 1000.0;
timings.add(elapsed);
logger.info(String.format(" -> Elapsed time %.2f, averaging %.2f sec / seek for %d seeks%n",
elapsed, Utils.averageDouble(timings), timings.size()));
if ( ! success ) {
logger.error(String.format("Failured to seek to %s from %s%n", targetContig.getSequenceName(), lastContig ));
}
//System.exit(1);
}
}
System.exit(1);
// code for randomly sampling the seeks
// Random rnd = new Random();
// String lastContig = null;
// List<Double> timings = new ArrayList<Double>();
// final int N_SAMPLES = 1000;
// //try { refFile.seekToContig("chr3"); } catch ( IOException e ) {}
// for ( int i = 0; i < N_SAMPLES; i++ ) {
// final int nextIndex = rnd.nextInt(refContigs.size());
// String nextContig = refFile.getSequenceDictionary().getSequence(nextIndex).getSequenceName();
// //nextContig = "chr2";
// try {
// System.out.printf("Seeking: current=%s, target=%s%n", refFile.getContigName(), nextContig);
// long lastTime = System.currentTimeMillis();
// final boolean success = refFile.seekToContig(nextContig, true);
// long curTime = System.currentTimeMillis();
// final double elapsed = (curTime - lastTime) / 1000.0;
// timings.add(elapsed);
// System.out.printf(" -> Elapsed time %.2f, averaging %.2f sec / seek for %d seeks%n",
// elapsed, Utils.averageDouble(timings), timings.size());
//
// if ( ! success ) {
// System.out.printf("Failured to seek to %s from %s%n", nextContig, lastContig );
// }
// //System.exit(1);
// } catch ( IOException e ) {
// System.out.printf("Failured to seek to %s from %s%n", nextContig, lastContig );
// e.printStackTrace();
// }
//
// lastContig = nextContig;
// }
// System.exit(1);
/*
final String targetChr = "chr10";
try {
refFile.seekToContig(targetChr);
} catch ( IOException e ){
System.out.printf("Failured to seek to %s%n", targetChr);
e.printStackTrace();
}
System.exit(1);
*/
//List<Double> timings = new ArrayList<Double>();
final long startTime = System.currentTimeMillis();
long lastTime = System.currentTimeMillis();
int i = 0;
String prevNextContigName = null;
logger.info(String.format("Walking reference sequence:%n"));
for ( SAMSequenceRecord refContig: refContigs ) {
long curTime = System.currentTimeMillis();
ReferenceSequence contig = refFile.nextSequence();
final double elapsed = (curTime - lastTime) / 1000.0;
timings.add(elapsed);
logger.info(String.format("%2d : expected %s contig, found %s with next of %s after %.2f seconds, average is %.2f%n", i,
refContig.getSequenceName(), contig.getName(), refFile.getNextContigName(), elapsed, Utils.averageDouble(timings)));
if ( prevNextContigName != null && contig.getName() != null && ! prevNextContigName.equals(contig.getName()) )
throw new RuntimeIOException(String.format("Unexpected contig ordering %s was expected next, but I found %s?",
prevNextContigName, contig.getName()));
prevNextContigName = refFile.getNextContigName();
lastTime = curTime;
i++;
logger.info(String.format(" Traversing from chr1 to %s would require jumping %d bytes%n",
contig.getName(), refFile.getDistanceBetweenContigs("chr1", contig.getName())));
}
}
public SAMFileReader getSamReader() { return this.engine.getSamReader(); }
public TraversalEngine getEngine() { return this.engine; }