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Code supporting SSG proof-of-concept shared memory parallelism. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1765 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-10-05 18:56:16 +00:00
parent fb619bd593
commit 8a503c86b6
1 changed files with 31 additions and 13 deletions
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44
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java
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@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters; import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -16,7 +17,7 @@ import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
import java.io.File; import java.io.File;
@ReadFilters(ZeroMappingQualityReadFilter.class) @ReadFilters(ZeroMappingQualityReadFilter.class)
public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSampleGenotyper.CallResult> { public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSampleGenotyper.CallResult> implements TreeReducible<SingleSampleGenotyper.CallResult> {
// Control output settings // Control output settings
@Argument(fullName = "variants_out", shortName = "varout", doc = "File to which variants should be written", required = false) @Argument(fullName = "variants_out", shortName = "varout", doc = "File to which variants should be written", required = false)
public File VARIANTS_FILE = null; public File VARIANTS_FILE = null;
@ -47,17 +48,16 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
@Argument(fullName = "disableCache", doc = "[ADVANCED] If true, we won't use the caching system. This argument is for testing purposes only", required = false) @Argument(fullName = "disableCache", doc = "[ADVANCED] If true, we won't use the caching system. This argument is for testing purposes only", required = false)
public boolean disableCache = false; public boolean disableCache = false;
/**
* Writer for genotype data.
*/
private GenotypeWriter genotypeWriter;
public class CallResult { public class CallResult {
long nConfidentCalls = 0; long nConfidentCalls = 0;
long nNonConfidentCalls = 0; long nNonConfidentCalls = 0;
long nCalledBases = 0; long nCalledBases = 0;
GenotypeWriter writer;
CallResult(GenotypeWriter writer) {
this.writer = writer;
}
public String toString() { public String toString() {
return String.format("SSG: %d confident and %d non-confident calls were made at %d bases", return String.format("SSG: %d confident and %d non-confident calls were made at %d bases",
nConfidentCalls, nNonConfidentCalls, nCalledBases); nConfidentCalls, nNonConfidentCalls, nCalledBases);
@ -80,7 +80,10 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
/** Initialize the walker with some sensible defaults */ /** Initialize the walker with some sensible defaults */
public void initialize() { public void initialize() {
//GenotypeLikelihoods.clearCache(); //GenotypeLikelihoods.clearCache();
// nothing to do if ( VARIANTS_FILE != null )
genotypeWriter = GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE);
else
genotypeWriter = GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out);
} }
/** /**
@ -138,10 +141,7 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
* @return an empty string * @return an empty string
*/ */
public CallResult reduceInit() { public CallResult reduceInit() {
if ( VARIANTS_FILE != null ) return new CallResult();
return new CallResult(GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE));
else
return new CallResult(GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out));
} }
/** /**
@ -160,16 +160,34 @@ public class SingleSampleGenotyper extends LocusWalker<SSGenotypeCall, SingleSam
if (confidence >= LOD_THRESHOLD) { if (confidence >= LOD_THRESHOLD) {
sum.nConfidentCalls++; sum.nConfidentCalls++;
//System.out.printf("Call %s%n", call); //System.out.printf("Call %s%n", call);
sum.writer.addGenotypeCall(call); genotypeWriter.addGenotypeCall(call);
} else } else
sum.nNonConfidentCalls++; sum.nNonConfidentCalls++;
} }
return sum; return sum;
} }
/**
* Combine adjacent call results.
*
* @param lhs first set of partial call results from genotyper; guaranteed to have come from 'earlier' in genome.
* @param rhs second set of partial call results from genotyper; guaranteed to have come from 'later' in genome.
*
* @return combined call results.
*/
public CallResult treeReduce( CallResult lhs, CallResult rhs ) {
CallResult combined = new CallResult();
combined.nCalledBases = lhs.nCalledBases + rhs.nCalledBases;
combined.nConfidentCalls = lhs.nConfidentCalls + rhs.nConfidentCalls;
combined.nNonConfidentCalls = lhs.nNonConfidentCalls + rhs.nNonConfidentCalls;
return combined;
}
/** Close the variant file. */ /** Close the variant file. */
public void onTraversalDone(CallResult sum) { public void onTraversalDone(CallResult sum) {
sum.writer.close(); // If the VARIANTS_FILE is null, the GATK is managing the output stream. Close the file.
if ( VARIANTS_FILE == null )
genotypeWriter.close();
} }
} }