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Refactor updateReadStates into PerSampleReadStateManager, add tracking of downsampling rate

This commit is contained in:
Mark DePristo 2013-01-13 12:23:51 -05:00
parent a4334a67e0
commit 5c2799554a
2 changed files with 55 additions and 19 deletions
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4
public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java
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@ -63,6 +63,8 @@ public class LIBSPerformance extends CommandLineProgram {
@Argument(fullName = "L", shortName = "L", doc = "Query location", required = false)
public String location = null;
@Argument(fullName = "dt", shortName = "dt", doc = "Enable downsampling", required = false)
public boolean downsample = false;
@Override
public int execute() throws IOException {
@ -86,7 +88,7 @@ public class LIBSPerformance extends CommandLineProgram {
for ( final SAMReadGroupRecord rg : reader.getFileHeader().getReadGroups() )
samples.add(rg.getSample());
final LIBSDownsamplingInfo ds = new LIBSDownsamplingInfo(false, -1);
final LIBSDownsamplingInfo ds = new LIBSDownsamplingInfo(downsample, 250);
final LocusIteratorByState libs =
new LocusIteratorByState(

70
public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java
View File

@ -29,6 +29,7 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.picard.util.PeekableIterator;
import net.sf.samtools.CigarOperator;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.downsampling.Downsampler;
import org.broadinstitute.sting.gatk.downsampling.LevelingDownsampler;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -50,6 +51,8 @@ import java.util.*;
* Time: 2:02 PM
*/
final class ReadStateManager implements Iterable<Map.Entry<String, ReadStateManager.PerSampleReadStateManager>> {
private final static Logger logger = Logger.getLogger(ReadStateManager.class);
private final static boolean CAPTURE_DOWNSAMPLING_STATS = true;
private final List<String> samples;
private final PeekableIterator<GATKSAMRecord> iterator;
private final SamplePartitioner<GATKSAMRecord> samplePartitioner;
@ -138,18 +141,8 @@ final class ReadStateManager implements Iterable<Map.Entry<String, ReadStateMana
* of the next pileup.
*/
public void updateReadStates() {
for (final PerSampleReadStateManager readStateManager : readStatesBySample.values() ) {
final Iterator<AlignmentStateMachine> it = readStateManager.iterator();
while (it.hasNext()) {
final AlignmentStateMachine state = it.next();
final CigarOperator op = state.stepForwardOnGenome();
if (op == null) {
// we discard the read only when we are past its end AND indel at the end of the read (if any) was
// already processed. Keeping the read state that returned null upon stepForwardOnGenome() is safe
// as the next call to stepForwardOnGenome() will return null again AND will clear hadIndel() flag.
it.remove(); // we've stepped off the end of the object
}
}
for (final PerSampleReadStateManager perSampleReadStateManager : readStatesBySample.values() ) {
perSampleReadStateManager.updateReadStates();
}
}
@ -301,13 +294,17 @@ final class ReadStateManager implements Iterable<Map.Entry<String, ReadStateMana
}
// TODO -- refactor into separate class with pointer to ReadStateManager for updates to the total counts
protected class PerSampleReadStateManager implements Iterable<AlignmentStateMachine> {
protected final class PerSampleReadStateManager implements Iterable<AlignmentStateMachine> {
private List<LinkedList<AlignmentStateMachine>> readStatesByAlignmentStart = new LinkedList<LinkedList<AlignmentStateMachine>>();
private final Downsampler<LinkedList<AlignmentStateMachine>> levelingDownsampler;
private int thisSampleReadStates = 0;
private final int downsamplingTarget;
private int nSitesNeedingDownsampling = 0;
private int nSites = 0;
public PerSampleReadStateManager(final LIBSDownsamplingInfo LIBSDownsamplingInfo) {
this.downsamplingTarget = LIBSDownsamplingInfo.isPerformDownsampling() ? LIBSDownsamplingInfo.getToCoverage() : -1;
this.levelingDownsampler = LIBSDownsamplingInfo.isPerformDownsampling()
? new LevelingDownsampler<LinkedList<AlignmentStateMachine>, AlignmentStateMachine>(LIBSDownsamplingInfo.getToCoverage())
: null;
@ -326,7 +323,8 @@ final class ReadStateManager implements Iterable<Map.Entry<String, ReadStateMana
thisSampleReadStates += states.size();
totalReadStates += states.size();
if ( levelingDownsampler != null ) {
if ( isDownsampling() ) {
captureDownsamplingStats();
levelingDownsampler.submit(readStatesByAlignmentStart);
levelingDownsampler.signalEndOfInput();
@ -339,6 +337,28 @@ final class ReadStateManager implements Iterable<Map.Entry<String, ReadStateMana
}
}
private boolean isDownsampling() {
return levelingDownsampler != null;
}
@Requires("isDownsampling()")
private void captureDownsamplingStats() {
if ( CAPTURE_DOWNSAMPLING_STATS ) {
nSites++;
final int loc = getFirst().getGenomePosition();
String message = "Pass through";
final boolean downsampling = thisSampleReadStates > downsamplingTarget;
if ( downsampling ) {
nSitesNeedingDownsampling++;
message = "Downsampling";
}
if ( downsampling || nSites % 10000 == 0 )
logger.info(String.format("%20s at %s: coverage=%d, max=%d, fraction of downsampled sites=%.2e",
message, loc, thisSampleReadStates, downsamplingTarget, (1.0 * nSitesNeedingDownsampling / nSites)));
}
}
public boolean isEmpty() {
return readStatesByAlignmentStart.isEmpty();
}
@ -351,11 +371,25 @@ final class ReadStateManager implements Iterable<Map.Entry<String, ReadStateMana
return thisSampleReadStates;
}
public void updateReadStates() {
final Iterator<AlignmentStateMachine> it = iterator();
while (it.hasNext()) {
final AlignmentStateMachine state = it.next();
final CigarOperator op = state.stepForwardOnGenome();
if (op == null) {
// we discard the read only when we are past its end AND indel at the end of the read (if any) was
// already processed. Keeping the read state that returned null upon stepForwardOnGenome() is safe
// as the next call to stepForwardOnGenome() will return null again AND will clear hadIndel() flag.
it.remove(); // we've stepped off the end of the object
}
}
}
public Iterator<AlignmentStateMachine> iterator() {
return new Iterator<AlignmentStateMachine>() {
private Iterator<LinkedList<AlignmentStateMachine>> alignmentStartIterator = readStatesByAlignmentStart.iterator();
private LinkedList<AlignmentStateMachine> currentPositionReadStates = null;
private Iterator<AlignmentStateMachine> currentPositionReadStatesIterator = null;
private final Iterator<LinkedList<AlignmentStateMachine>> alignmentStartIterator = readStatesByAlignmentStart.iterator();
private LinkedList<AlignmentStateMachine> currentPositionReadStates;
private Iterator<AlignmentStateMachine> currentPositionReadStatesIterator;
public boolean hasNext() {
return alignmentStartIterator.hasNext() ||