zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added a definitely inappropriately placed testing of the new fasta seeking system at the bottom of the file -- it's not called but it probably should be moved to somewhere more appropriate. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@141 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-22 19:57:52 +00:00
parent 611ab0bdb3
commit 1df23b0417
1 changed files with 124 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

125
core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
View File

@ -2,20 +2,28 @@ package org.broadinstitute.sting.gatk;
import net.sf.samtools.SAMFileReader.ValidationStringency;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.RuntimeIOException;
import edu.mit.broad.picard.cmdline.CommandLineProgram;
import edu.mit.broad.picard.cmdline.Usage;
import edu.mit.broad.picard.cmdline.Option;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.rodGFF;
import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import java.io.*;
import java.util.*;
import java.util.List;
import java.util.ArrayList;
import java.util.Random;
public class GenomeAnalysisTK extends CommandLineProgram {
// Usage and parameters
@ -51,6 +59,8 @@ public class GenomeAnalysisTK extends CommandLineProgram {
protected int doWork() {
walkerManager = new WalkerManager(pluginPathName);
//testNewReferenceFeatures(REF_FILE_ARG);
final boolean TEST_ROD = false;
ReferenceOrderedData[] rods = null;
@ -117,8 +127,9 @@ public class GenomeAnalysisTK extends CommandLineProgram {
engine.setSortOnFly(ENABLED_SORT_ON_FLY.toLowerCase().equals("true"));
engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true"));
//engine.testReference();
//LocusWalker<Integer,Integer> walker = new PileupWalker();
// Try to get the walker specified
@ -142,4 +153,116 @@ public class GenomeAnalysisTK extends CommandLineProgram {
return 0;
}
/**
* 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);
Utils.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);
System.out.printf("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);
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", 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;
System.out.printf("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);
System.out.printf("%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++;
System.out.printf(" Traversing from chr1 to %s would require jumping %d bytes%n",
contig.getName(), refFile.getDistanceBetweenContigs("chr1", contig.getName()));
}
}
}