add fast gather to UG; change UG to work with log-lessHMM (work in prograss)
This commit is contained in:
Ami Levy-Moonshine
parent
6bf31065e3
commit
6590039bc3
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@ -27,18 +27,17 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.Haplotype;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.sting.utils.pairhmm.*;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.PrintStream;
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import java.util.*;
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public class LikelihoodCalculationEngine {
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@ -98,12 +97,12 @@ public class LikelihoodCalculationEngine {
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for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
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//if( DEBUG ) { System.out.println("Evaluating sample " + sample + " with " + perSampleReadList.get( sample ).size() + " passing reads"); }
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// evaluate the likelihood of the reads given those haplotypes
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stratifiedReadMap.put(sampleEntry.getKey(), computeReadLikelihoods(haplotypes, sampleEntry.getValue(), sampleEntry.getKey()));
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stratifiedReadMap.put(sampleEntry.getKey(), computeReadLikelihoods(haplotypes, sampleEntry.getValue()));
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}
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return stratifiedReadMap;
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}
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private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final ArrayList<GATKSAMRecord> reads, final String sample ) {
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private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final ArrayList<GATKSAMRecord> reads) {
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final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
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final int numHaplotypes = haplotypes.size();
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@ -195,7 +195,7 @@ public abstract class CommandLineProgram {
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clp.setupLoggerLevel(layout);
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Class[] argumentSources = clp.getArgumentSources();
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for (Class argumentSource : argumentSources)
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for (Class argumentSource : argumentSources)
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parser.addArgumentSource(clp.getArgumentSourceName(argumentSource), argumentSource);
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parsedArgs = parser.parse(args);
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@ -35,5 +35,6 @@ import java.lang.annotation.*;
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@Target({ElementType.FIELD})
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public @interface Gather {
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Class value() default Gather.class;
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String className() default "";
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boolean enabled() default true;
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}
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@ -45,6 +45,7 @@ import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
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import org.broadinstitute.sting.utils.pairhmm.PairHMM;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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@ -157,9 +158,11 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
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/**
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* A raw, unfiltered, highly sensitive callset in VCF format.
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*/
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@Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") //TODO: check this gatherer
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@Output(doc="File to which variants should be written",required=true)
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protected VariantContextWriter writer = null;
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@Hidden
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@Argument(fullName = "debug_file", shortName = "debug_file", doc = "File to print all of the annotated and detailed debugging output", required = false)
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protected PrintStream verboseWriter = null;
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.clipping.ReadClipper;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.pairhmm.ExactPairHMM;
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import org.broadinstitute.sting.utils.pairhmm.LoglessCachingPairHMM;
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import org.broadinstitute.sting.utils.pairhmm.OriginalPairHMM;
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import org.broadinstitute.sting.utils.pairhmm.PairHMM;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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@ -101,6 +102,8 @@ public class PairHMMIndelErrorModel {
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break;
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case CACHING:
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case LOGLESS_CACHING:
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pairHMM = new LoglessCachingPairHMM();
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break;
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default:
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throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL and EXACT.");
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}
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@ -371,7 +374,7 @@ public class PairHMMIndelErrorModel {
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readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
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(read.hasBaseIndelQualities() ? read.getBaseInsertionQualities() : contextLogGapOpenProbabilities),
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(read.hasBaseIndelQualities() ? read.getBaseDeletionQualities() : contextLogGapOpenProbabilities),
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contextLogGapContinuationProbabilities, startIndexInHaplotype, false);
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contextLogGapContinuationProbabilities, startIndexInHaplotype, previousHaplotypeSeen == null);
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if (DEBUG) {
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@ -204,7 +204,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
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if ( PRIORITY_STRING == null && genotypeMergeOption == null) {
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genotypeMergeOption = VariantContextUtils.GenotypeMergeType.UNSORTED;
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//PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); Deleted by Ami (7/10/12)
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logger.info("Priority string not provided, using arbitrary genotyping order: "+priority);
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logger.info("Priority string is not provided, using arbitrary genotyping order: "+priority);
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}
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samples = sitesOnlyVCF ? Collections.<String>emptySet() : SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
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@ -23,7 +23,6 @@
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*/
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package org.broadinstitute.sting.queue.extensions.gatk;
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import net.sf.samtools.BAMIndex;
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import net.sf.samtools.SAMFileWriter;
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import org.broad.tribble.Tribble;
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@ -119,9 +118,14 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
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List<ArgumentField> argumentFields = new ArrayList<ArgumentField>();
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for (ArgumentSource argumentSource: parsingEngine.extractArgumentSources(classType))
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if (!argumentSource.isDeprecated()) {
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Class<?> gatherer = null;
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if (argumentSource.field.isAnnotationPresent(Gather.class))
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gatherer = argumentSource.field.getAnnotation(Gather.class).value();
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String gatherer = null;
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if (argumentSource.field.isAnnotationPresent(Gather.class)) {
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Gather gather = argumentSource.field.getAnnotation(Gather.class);
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if(! "".equals(gather.className()))
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gatherer = gather.className();
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else
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gatherer = gather.value().getName();
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}
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for (ArgumentDefinition argumentDefinition: argumentSource.createArgumentDefinitions())
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argumentFields.addAll(getArgumentFields(argumentDefinition, gatherer));
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}
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@ -130,7 +134,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
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private static final List<String> intervalFields = Arrays.asList("intervals", "excludeIntervals", "targetIntervals");
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private static List<? extends ArgumentField> getArgumentFields(ArgumentDefinition argumentDefinition, Class<?> gatherer) {
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private static List<? extends ArgumentField> getArgumentFields(ArgumentDefinition argumentDefinition, String gatherer) {
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if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
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return Arrays.asList(
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new IntervalFileArgumentField(argumentDefinition),
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@ -154,7 +158,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
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String gatherClass;
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if (gatherer != null)
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gatherClass = gatherer.getName();
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gatherClass = gatherer;
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else if (SAMFileWriter.class.isAssignableFrom(argumentDefinition.argumentType))
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gatherClass = "BamGatherFunction";
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else if (VariantContextWriter.class.isAssignableFrom(argumentDefinition.argumentType))
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@ -195,6 +195,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
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private static final List<String> gatkPackages = Arrays.asList(
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"org.broadinstitute.sting.gatk",
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"org.broadinstitute.sting.pipeline",
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"org.broadinstitute.sting.tools",
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"org.broadinstitute.sting.gatk.datasources.reads.utilities");
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/**
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