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same commit as yesterday, since I moved to he new computer

This commit is contained in:
Ami Levy-Moonshine 2013-01-07 13:55:29 -05:00
parent 10a705b27f 2018285a39
commit b5faf00fce
9 changed files with 59 additions and 13 deletions
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8
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -28,7 +28,9 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pairhmm.*;
@ -95,12 +97,12 @@ public class LikelihoodCalculationEngine {
for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
//if( DEBUG ) { System.out.println("Evaluating sample " + sample + " with " + perSampleReadList.get( sample ).size() + " passing reads"); }
// evaluate the likelihood of the reads given those haplotypes
stratifiedReadMap.put(sampleEntry.getKey(), computeReadLikelihoods(haplotypes, sampleEntry.getValue(), sampleEntry.getKey()));
stratifiedReadMap.put(sampleEntry.getKey(), computeReadLikelihoods(haplotypes, sampleEntry.getValue()));
}
return stratifiedReadMap;
}
private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final ArrayList<GATKSAMRecord> reads, final String sample ) {
private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final ArrayList<GATKSAMRecord> reads) {
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
final int numHaplotypes = haplotypes.size();

2
public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
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@ -195,7 +195,7 @@ public abstract class CommandLineProgram {
clp.setupLoggerLevel(layout);
Class[] argumentSources = clp.getArgumentSources();
for (Class argumentSource : argumentSources)
for (Class argumentSource : argumentSources)
parser.addArgumentSource(clp.getArgumentSourceName(argumentSource), argumentSource);
parsedArgs = parser.parse(args);

1
public/java/src/org/broadinstitute/sting/commandline/Gather.java
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@ -35,5 +35,6 @@ import java.lang.annotation.*;
@Target({ElementType.FIELD})
public @interface Gather {
Class value() default Gather.class;
String className() default "";
boolean enabled() default true;
}

3
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -50,6 +50,7 @@ import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.PrintStream;
import java.util.*;
@ -157,9 +158,11 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
/**
* A raw, unfiltered, highly sensitive callset in VCF format.
*/
@Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") //TODO: check this gatherer
@Output(doc="File to which variants should be written",required=true)
protected VariantContextWriter writer = null;
@Hidden
@Argument(fullName = "debug_file", shortName = "debug_file", doc = "File to print all of the annotated and detailed debugging output", required = false)
protected PrintStream verboseWriter = null;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pairhmm.ExactPairHMM;
import org.broadinstitute.sting.utils.pairhmm.LoglessCachingPairHMM;
import org.broadinstitute.sting.utils.pairhmm.OriginalPairHMM;
import org.broadinstitute.sting.utils.pairhmm.PairHMM;
import org.broadinstitute.sting.utils.pileup.PileupElement;
@ -101,8 +102,11 @@ public class PairHMMIndelErrorModel {
break;
case CACHING:
case LOGLESS_CACHING:
pairHMM = new LoglessCachingPairHMM();
System.err.println("warning: this option (LOGLESS_CACHING in UG) is still under development");
break;
default:
throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL and EXACT.");
throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL, EXACT or LOGLESS_CACHING (the third option is still under development).");
}
// fill gap penalty table, affine naive model:
@ -332,6 +336,7 @@ public class PairHMMIndelErrorModel {
getContextHomopolymerLength(readBases,hrunProfile);
fillGapProbabilities(hrunProfile, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities);
boolean firstHap = true;
for (Allele a: haplotypeMap.keySet()) {
Haplotype haplotype = haplotypeMap.get(a);
@ -371,7 +376,7 @@ public class PairHMMIndelErrorModel {
readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
(read.hasBaseIndelQualities() ? read.getBaseInsertionQualities() : contextLogGapOpenProbabilities),
(read.hasBaseIndelQualities() ? read.getBaseDeletionQualities() : contextLogGapOpenProbabilities),
contextLogGapContinuationProbabilities, startIndexInHaplotype, false);
contextLogGapContinuationProbabilities, startIndexInHaplotype, firstHap);
if (DEBUG) {
@ -383,6 +388,7 @@ public class PairHMMIndelErrorModel {
perReadAlleleLikelihoodMap.add(p, a, readLikelihood);
readLikelihoods[readIdx][j++] = readLikelihood;
firstHap = false;
}
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -205,7 +205,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
if ( PRIORITY_STRING == null && genotypeMergeOption == null) {
genotypeMergeOption = VariantContextUtils.GenotypeMergeType.UNSORTED;
//PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); Deleted by Ami (7/10/12)
logger.info("Priority string not provided, using arbitrary genotyping order: "+priority);
logger.info("Priority string is not provided, using arbitrary genotyping order: "+priority);
}
samples = sitesOnlyVCF ? Collections.<String>emptySet() : SampleUtils.getSampleList(vcfRods, genotypeMergeOption);

16
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
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@ -23,7 +23,6 @@
*/
package org.broadinstitute.sting.queue.extensions.gatk;
import net.sf.samtools.BAMIndex;
import net.sf.samtools.SAMFileWriter;
import org.broad.tribble.Tribble;
@ -119,9 +118,14 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
List<ArgumentField> argumentFields = new ArrayList<ArgumentField>();
for (ArgumentSource argumentSource: parsingEngine.extractArgumentSources(classType))
if (!argumentSource.isDeprecated()) {
Class<?> gatherer = null;
if (argumentSource.field.isAnnotationPresent(Gather.class))
gatherer = argumentSource.field.getAnnotation(Gather.class).value();
String gatherer = null;
if (argumentSource.field.isAnnotationPresent(Gather.class)) {
Gather gather = argumentSource.field.getAnnotation(Gather.class);
if(! "".equals(gather.className()))
gatherer = gather.className();
else
gatherer = gather.value().getName();
}
for (ArgumentDefinition argumentDefinition: argumentSource.createArgumentDefinitions())
argumentFields.addAll(getArgumentFields(argumentDefinition, gatherer));
}
@ -130,7 +134,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
private static final List<String> intervalFields = Arrays.asList("intervals", "excludeIntervals", "targetIntervals");
private static List<? extends ArgumentField> getArgumentFields(ArgumentDefinition argumentDefinition, Class<?> gatherer) {
private static List<? extends ArgumentField> getArgumentFields(ArgumentDefinition argumentDefinition, String gatherer) {
if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
return Arrays.asList(
new IntervalFileArgumentField(argumentDefinition),
@ -154,7 +158,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
String gatherClass;
if (gatherer != null)
gatherClass = gatherer.getName();
gatherClass = gatherer;
else if (SAMFileWriter.class.isAssignableFrom(argumentDefinition.argumentType))
gatherClass = "BamGatherFunction";
else if (VariantContextWriter.class.isAssignableFrom(argumentDefinition.argumentType))

1
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
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@ -196,6 +196,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
"org.broadinstitute.sting.tools",
"org.broadinstitute.sting.gatk",
"org.broadinstitute.sting.pipeline",
"org.broadinstitute.sting.tools",
"org.broadinstitute.sting.gatk.datasources.reads.utilities");
/**

29
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala 100644
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@ -0,0 +1,29 @@
package org.broadinstitute.sting.queue.extensions.gatk
import org.broadinstitute.sting.queue.function.{RetryMemoryLimit, JavaCommandLineFunction}
import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
import org.broadinstitute.sting.queue.util.ClassFieldCache
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor
/**
* Created with IntelliJ IDEA.
* User: ami
* Date: 12/11/12
* Time: 2:04 PM
* To change this template use File | Settings | File Templates.
*/
class CatVariantsGatherer extends CatVariants with GatherFunction with RetryMemoryLimit{
this.assumeSorted = true
private lazy val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
override def freezeFieldValues() {
this.reference = originalGATK.reference_sequence
this.variant = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) }
this.outputFile = this.originalOutput
super.freezeFieldValues()
}
}