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Backporting LIBSPerformance improvements to original commit

This commit is contained in:
Mark DePristo 2013-01-13 09:53:10 -05:00
parent a7fe334a3f
commit 3a6b4b43b7
1 changed files with 8 additions and 5 deletions
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13
public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java
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@ -37,10 +37,7 @@ import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.iterators.GATKSAMIterator; import org.broadinstitute.sting.gatk.iterators.GATKSAMIterator;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -100,12 +97,18 @@ public class LIBSPerformance extends CommandLineProgram {
samples, samples,
false); false);
final SimpleTimer timer = new SimpleTimer().start();
int bp = 0; int bp = 0;
double lastElapsed = 0;
while ( libs.hasNext() ) { while ( libs.hasNext() ) {
AlignmentContext context = libs.next(); AlignmentContext context = libs.next();
if ( ++bp % 100000 == 0 ) bp++;
if ( timer.getElapsedTime() - lastElapsed > 10 ) {
logger.info(bp + " iterations at " + context.getLocation()); logger.info(bp + " iterations at " + context.getLocation());
lastElapsed = timer.getElapsedTime();
}
} }
logger.info(String.format("runtime in seconds: %.2f", timer.getElapsedTime()));
return 0; return 0;
} }