add fast gather to UG; change UG to work with log-lessHMM (work in prograss)

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java

@@ -27,18 +27,17 @@ 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.Haplotype;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
+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.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.pairhmm.*;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.PrintStream;
 import java.util.*;
 
 public class LikelihoodCalculationEngine {
@@ -98,12 +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();

public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -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);
 

public/java/src/org/broadinstitute/sting/commandline/Gather.java

@@ -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;
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -45,6 +45,7 @@ import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.sting.utils.pairhmm.PairHMM;
 import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -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;

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java

@@ -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;
@@ -101,6 +102,8 @@ public class PairHMMIndelErrorModel {
                 break;
             case CACHING:
             case LOGLESS_CACHING:
+                pairHMM = new LoglessCachingPairHMM();
+                break;
             default:
                 throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL and EXACT.");
         }
@@ -371,7 +374,7 @@ public class PairHMMIndelErrorModel {
                         readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals,
                                 (read.hasBaseIndelQualities() ? read.getBaseInsertionQualities() : contextLogGapOpenProbabilities),
                                 (read.hasBaseIndelQualities() ? read.getBaseDeletionQualities() : contextLogGapOpenProbabilities),
-                                contextLogGapContinuationProbabilities, startIndexInHaplotype, false);
+                                contextLogGapContinuationProbabilities, startIndexInHaplotype, previousHaplotypeSeen == null);
 
 
                         if (DEBUG) {

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java

@@ -204,7 +204,7 @@ 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);

public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java

@@ -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;
+                String gatherer = null;
-                if (argumentSource.field.isAnnotationPresent(Gather.class))
+                if (argumentSource.field.isAnnotationPresent(Gather.class)) {
-                    gatherer = argumentSource.field.getAnnotation(Gather.class).value();
+                    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))

public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java

@@ -195,6 +195,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
     private static final List<String> gatkPackages = Arrays.asList(
             "org.broadinstitute.sting.gatk",
             "org.broadinstitute.sting.pipeline",
+            "org.broadinstitute.sting.tools",
             "org.broadinstitute.sting.gatk.datasources.reads.utilities");
 
     /**