Mlc debug no space left on device

.gitattributes

@@ -5,8 +5,7 @@ src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38
 src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38 -filter=lfs -diff=lfs -merge=lfs -text
 src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38 -filter=lfs -diff=lfs -merge=lfs -text
 src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38 -filter=lfs -diff=lfs -merge=lfs -text
-
 #Otherwise, track everything in large
 src/test/resources/large/** filter=lfs diff=lfs merge=lfs -text
 src/main/resources/large/** filter=lfs diff=lfs merge=lfs -text
-
+*.psd filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -22,6 +22,7 @@ out/
 gatkcondaenv.yml
 gatkcondaenv.intel.yml
 gatkPythonPackageArchive.zip
+testfiles/
 
 #Please don't commit me
 client_secret.json

src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/IntervalArgumentCollection.java

@@ -241,6 +241,17 @@ private TraversalParameters parseIntervals(final GenomeLocParser genomeLocParser
     }
 
 
+    /**
+     * Is the interval specified an interval list
+     */
+    public String intervalListFileSpecified() {
+        if (getIntervalStrings().size()==1 && IntervalUtils.isGatkIntervalFile(getIntervalStrings().get(0))) {
+            return getIntervalStrings().get(0);
+        } else {
+            return null;
+        }
+    }
+
     /**
      * Have any intervals been specified for inclusion or exclusion
      */

src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java

@@ -145,7 +145,7 @@ public abstract class GATKTool extends CommandLineProgram {
     /**
      * Our source of reference data (null if no reference was provided)
      */
-    ReferenceDataSource reference;
+    protected ReferenceDataSource reference;
 
     /**
      * Our source of reads data (null if no source of reads was provided)

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/AnnotationUtils.java

@@ -16,6 +16,7 @@ public final class AnnotationUtils {
     public static final String ALLELE_SPECIFIC_SPLIT_REGEX = "\\|"; //String.split takes a regex, so we need to escape the pipe
     public static final String BRACKET_REGEX = "\\[|\\]";
     public static final String LIST_DELIMITER = ",";
+    public static final String MISSING_VALUE = ".";
 
     private AnnotationUtils(){}
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java

@@ -107,9 +107,58 @@ public Map<String, Object> annotateRawData(final ReferenceContext ref,
     @Override
     @SuppressWarnings({"unchecked", "rawtypes"})//FIXME generics here blow up
     public Map<String, Object> combineRawData(List<Allele> allelesList, List<ReducibleAnnotationData<?>>  listOfRawData) {
-        return null;
+        //VC already contains merged alleles from ReferenceConfidenceVariantContextMerger
+        ReducibleAnnotationData<Integer> combinedData = new AlleleSpecificAnnotationData(allelesList, null);
+
+        for (final ReducibleAnnotationData<?> currentValue : listOfRawData) {
+            ReducibleAnnotationData<Integer> value = (ReducibleAnnotationData<Integer>)currentValue;
+            parseRawDataString(value);
+            combineAttributeMap(value, combinedData);
+        }
+        final Map<String, Object> annotations = new HashMap<>();
+        String annotationString = makeRawAnnotationString(allelesList, combinedData.getAttributeMap());
+        annotations.put(getPrimaryRawKey(), annotationString);
+        return annotations;
+    }
+
+    protected void parseRawDataString(final ReducibleAnnotationData<Integer> myData) {
+        final String rawDataString = myData.getRawData();
+        //get per-allele data by splitting on allele delimiter
+        final String[] rawDataPerAllele = rawDataString.split(AnnotationUtils.ALLELE_SPECIFIC_SPLIT_REGEX);
+        for (int i=0; i<rawDataPerAllele.length; i++) {
+            final String alleleData = rawDataPerAllele[i];
+            myData.putAttribute(myData.getAlleles().get(i), (alleleData.isEmpty() || alleleData.equals(AnnotationUtils.MISSING_VALUE)) ? null : Integer.parseInt(alleleData));
+        }
     }
 
+    public void combineAttributeMap(final ReducibleAnnotationData<Integer> toAdd, final ReducibleAnnotationData<Integer> combined) {
+        //check that alleles match
+        for (final Allele currentAllele : combined.getAlleles()){
+            //combined is initialized with all alleles, but toAdd might have only a subset
+            if (toAdd.getAttribute(currentAllele) != null) {
+                if (toAdd.getAttribute(currentAllele) != null && combined.getAttribute(currentAllele) != null) {
+                    combined.putAttribute(currentAllele, (int)combined.getAttribute(currentAllele) + (int)toAdd.getAttribute(currentAllele));
+                } else {
+                    combined.putAttribute(currentAllele, toAdd.getAttribute(currentAllele));
+                }
+            }
+        }
+    }
+
+    private String makeRawAnnotationString(final List<Allele> vcAlleles, final Map<Allele, Integer> perAlleleValues) {
+        String annotationString = "";
+        for (final Allele current : vcAlleles) {
+            if (!annotationString.isEmpty()) {
+                annotationString += AnnotationUtils.ALLELE_SPECIFIC_RAW_DELIM;
+            }
+            if(perAlleleValues.get(current) != null) {
+                annotationString += String.format("%d", perAlleleValues.get(current));
+            } else {
+                annotationString += String.format("%d", 0);
+            }
+        }
+        return annotationString;
+    }
 
     /**
      * Uses the "AS_QUAL" key, which must be computed by the genotyping engine in GenotypeGVCFs, to

src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java

@@ -42,12 +42,17 @@ public final class GnarlyGenotyperEngine {
     private Set<Class<? extends InfoFieldAnnotation>> allASAnnotations;
 
     private final int maxAltAllelesToOutput;
+    private final boolean emitPls;
     private final boolean keepAllSites;
     private final boolean stripASAnnotations;
 
-
     public GnarlyGenotyperEngine(final boolean keepAllSites, final int maxAltAllelesToOutput, final boolean stripASAnnotations) {
+        this(keepAllSites, maxAltAllelesToOutput, true, stripASAnnotations);
+    }
+
+    public GnarlyGenotyperEngine(final boolean keepAllSites, final int maxAltAllelesToOutput, final boolean emitPls, final boolean stripASAnnotations) {
         this.maxAltAllelesToOutput = maxAltAllelesToOutput;
+        this.emitPls = emitPls;
         this.keepAllSites = keepAllSites;
         this.stripASAnnotations = stripASAnnotations;
 
@@ -180,7 +185,7 @@ else if (variant.hasAttribute(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY)) {
         //Get AC and SB annotations
         //remove the NON_REF allele and update genotypes if necessary
         final int[] rawGenotypeCounts = new int[3];
-        final GenotypesContext calledGenotypes = iterateOnGenotypes(variant, targetAlleles, alleleCountMap, SBsum, removeNonRef, variant.hasAttribute(GATKVCFConstants.RAW_GENOTYPE_COUNT_KEY) ? null : rawGenotypeCounts);
+        final GenotypesContext calledGenotypes = iterateOnGenotypes(variant, targetAlleles, alleleCountMap, SBsum, removeNonRef, emitPls, variant.hasAttribute(GATKVCFConstants.RAW_GENOTYPE_COUNT_KEY) ? null : rawGenotypeCounts);
         Integer numCalledAlleles = 0;
         if (variant.hasGenotypes()) {
             for (final Allele a : targetAlleles) {
@@ -304,9 +309,9 @@ else if (variant.hasAttribute(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY)) {
      */
     @VisibleForTesting
     protected GenotypesContext iterateOnGenotypes(final VariantContext vc, final List<Allele> targetAlleles,
-                                                  final Map<Allele, Integer> targetAlleleCounts, final int[] SBsum,
-                                                  final boolean nonRefReturned,
-                                                  final int[] rawGenotypeCounts) {
+                                                final Map<Allele, Integer> targetAlleleCounts, final int[] SBsum,
+                                                final boolean nonRefReturned, final boolean emitPLs,
+                                                final int[] rawGenotypeCounts) {
         final int maxAllelesToOutput = maxAltAllelesToOutput + 1;  //+1 for ref
         final List<Allele> inputAllelesWithNonRef = vc.getAlleles();
         if(nonRefReturned && !inputAllelesWithNonRef.get(inputAllelesWithNonRef.size()-1).equals(Allele.NON_REF_ALLELE)) {
@@ -347,7 +352,11 @@ else if (g.countAllele(Allele.NON_REF_ALLELE) > 0) {
             }
             if (g.hasPL()) {
                 final int[] PLs = trimPLs(g, newPLsize);
-                genotypeBuilder.PL(PLs);
+                if (emitPLs) {
+                    genotypeBuilder.PL(PLs);
+                } else {
+                    genotypeBuilder.noPL();
+                }
                 genotypeBuilder.GQ(MathUtils.secondSmallestMinusSmallest(PLs, 0));
                 //If GenomicsDB returns no-call genotypes like CombineGVCFs (depending on the GenomicsDBExportConfiguration),
                 // then we need to actually find the GT from PLs
@@ -527,4 +536,4 @@ private static int[] getSBFieldAsIntArray(Genotype g) {
           }
       }
     }
-}
+}

src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java

@@ -1570,7 +1570,7 @@ public static boolean isReciprocalOverlap(final SimpleInterval interval1, final
      * </p>
      *
      * @param input input collection of lacatables, may contain duplicates.
-     * @param dictionary the referene dictionary.
+     * @param dictionary the reference dictionary.
      * @param <L> the locatable type.
      * @throws IllegalArgumentException if input is {@code null}.
      * @return never {@code null}, but perhaps an empty map. It is guarantee that no value in the map is an empty list upon return.

src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryResultAndStatistics.java

@@ -0,0 +1,16 @@
+package org.broadinstitute.hellbender.utils.bigquery;
+
+import com.google.cloud.bigquery.JobStatistics;
+import com.google.cloud.bigquery.TableResult;
+
+public class BigQueryResultAndStatistics {
+    public final TableResult result;
+    public final JobStatistics.QueryStatistics queryStatistics;
+
+    public BigQueryResultAndStatistics(final TableResult result, final JobStatistics.QueryStatistics queryStatistics) {
+        this.result = result;
+        this.queryStatistics = queryStatistics;
+    }
+
+
+}