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