From b8367611047d622db5ffa74e53bd250838cbdd89 Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 28 Apr 2009 21:50:22 +0000 Subject: [PATCH] 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 --- .../sting/gatk/GenomeAnalysisTK.java | 115 ------------------ 1 file changed, 115 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 193b83773..063b5e643 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -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 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 timings = new ArrayList(); - 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 timings = new ArrayList(); -// 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 timings = new ArrayList(); - 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; }