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

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

@@ -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();

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

@@ -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;

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;
@@ -101,8 +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;
                     }
                 }
             }

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

@@ -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);

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

@@ -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");
 
     /**

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala

@@ -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()
+  }
+
+
+
+}