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Updating AlignmentStateMachinePerformance to include some more useful performance assessments

This commit is contained in:
Mark DePristo 2013-01-11 10:44:39 -05:00
parent 9e23c592e6
commit bd03511e35
1 changed files with 49 additions and 18 deletions
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67
public/java/test/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachinePerformance.java
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@ -26,6 +26,9 @@
package org.broadinstitute.sting.utils.locusiterator; package org.broadinstitute.sting.utils.locusiterator;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.locusiterator.old.SAMRecordAlignmentState; import org.broadinstitute.sting.utils.locusiterator.old.SAMRecordAlignmentState;
@ -33,6 +36,8 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Arrays; import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/** /**
* Caliper microbenchmark of fragment pileup * Caliper microbenchmark of fragment pileup
@ -42,33 +47,59 @@ public class AlignmentStateMachinePerformance {
final static int nReads = 10000; final static int nReads = 10000;
final static int locus = 1; final static int locus = 1;
private enum Op {
NEW_STATE, OLD_STATE, NEW_LIBS
}
public static void main(String[] args) { public static void main(String[] args) {
final int rep = Integer.valueOf(args[0]); final int rep = Integer.valueOf(args[0]);
final boolean useNew = Boolean.valueOf(args[1]); final Op op = Op.valueOf(args[1]);
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
final GenomeLocParser genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
int nIterations = 0; int nIterations = 0;
for ( final String cigar : Arrays.asList("101M", "50M10I40M", "50M10D40M") ) { for ( final String cigar : Arrays.asList("101M", "50M10I40M", "50M10D40M") ) {
for ( int j = 0; j < nReads; j++ ) { GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, locus, readLength);
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, locus, readLength); read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
read.setReadBases(Utils.dupBytes((byte) 'A', readLength)); final byte[] quals = new byte[readLength];
final byte[] quals = new byte[readLength]; for ( int i = 0; i < readLength; i++ )
for ( int i = 0; i < readLength; i++ ) quals[i] = (byte)(i % QualityUtils.MAX_QUAL_SCORE);
quals[i] = (byte)(i % QualityUtils.MAX_QUAL_SCORE); read.setBaseQualities(quals);
read.setBaseQualities(quals); read.setCigarString(cigar);
read.setCigarString(cigar);
for ( int j = 0; j < nReads; j++ ) {
for ( int i = 0; i < rep; i++ ) { for ( int i = 0; i < rep; i++ ) {
if ( useNew ) { switch ( op ) {
final AlignmentStateMachine alignmentStateMachine = new AlignmentStateMachine(read); case NEW_STATE:
while ( alignmentStateMachine.stepForwardOnGenome() != null ) { {
nIterations++; final AlignmentStateMachine alignmentStateMachine = new AlignmentStateMachine(read);
while ( alignmentStateMachine.stepForwardOnGenome() != null ) {
nIterations++;
}
} }
} else { break;
final SAMRecordAlignmentState alignmentStateMachine = new SAMRecordAlignmentState(read); case OLD_STATE:
while ( alignmentStateMachine.stepForwardOnGenome() != null ) { {
alignmentStateMachine.getRead(); final SAMRecordAlignmentState alignmentStateMachine = new SAMRecordAlignmentState(read);
nIterations++; while ( alignmentStateMachine.stepForwardOnGenome() != null ) {
alignmentStateMachine.getRead();
nIterations++;
}
}
break;
case NEW_LIBS:
{
final List<SAMRecord> reads = Collections.nCopies(30, (SAMRecord)read);
final org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState libs =
new org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState(
new LocusIteratorByStateBaseTest.FakeCloseableIterator<SAMRecord>(reads.iterator()),
LocusIteratorByStateBaseTest.createTestReadProperties(),
genomeLocParser,
LocusIteratorByStateBaseTest.sampleListForSAMWithoutReadGroups());
while ( libs.hasNext() ) {
AlignmentContext context = libs.next();
}
} }
} }
} }