starting to respond to review comments"

broadinstitute · Feb 23, 2022 · 1c6dc21 · 1c6dc21
1 parent 3e2785c
commit 1c6dc21
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Showing 3 changed files with 12 additions and 16 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/AssemblyRegionIterator.java b/src/main/java/org/broadinstitute/hellbender/engine/AssemblyRegionIterator.java
@@ -88,7 +88,7 @@ public AssemblyRegionIterator(final MultiIntervalShard<GATKRead> readShard,
         this.readCachingIterator = new ReadCachingIterator(readShard.iterator());
         this.readCache = new ArrayDeque<>();
         this.activityProfile = new BandPassActivityProfile(assemblyRegionArgs.maxProbPropagationDistance, assemblyRegionArgs.activeProbThreshold, BandPassActivityProfile.MAX_FILTER_SIZE, BandPassActivityProfile.DEFAULT_SIGMA, readHeader);
-        this.pendingAlignmentData = trackPileups? new ArrayDeque<>(): null;
+        this.pendingAlignmentData = trackPileups ? new ArrayDeque<>() : null;
 
         // We wrap our LocusIteratorByState inside an IntervalAlignmentContextIterator so that we get empty loci
         // for uncovered locations. This is critical for reproducing GATK 3.x behavior!
@@ -218,7 +218,8 @@ private void fillNextAssemblyRegionWithReads( final AssemblyRegion region ) {
     }
 
     private void fillNextAssemblyRegionWithPileupData(final AssemblyRegion region){
-        if (pendingAlignmentData==null){
+        // Save ourselves the memory footprint and work of saving the pileups in the event they aren't needed for processing.
+        if (pendingAlignmentData == null){
             return;
         }
         final List<AlignmentAndReferenceContext> overlappingAlignmentData = new ArrayList<>();

diff --git a/...institute/hellbender/tools/walkers/haplotypecaller/PileupDetectionArgumentCollection.java b/...institute/hellbender/tools/walkers/haplotypecaller/PileupDetectionArgumentCollection.java
@@ -19,7 +19,6 @@ public final class PileupDetectionArgumentCollection {
     //TODO we currently don't see the same threshold from active region determination...
     public static final String PILEUP_DETECTION_ACETIVE_REGION_LOD_THRESHOLD_LONG_NAME = "pileup-detection-active-region-lod-threshold";
 
-
     // Arguments related to DRAGEN heuristics related to "read badness" intended to filter out false positives from the pileup detection code
     public static final String PILEUP_DETECTION_BAD_READ_RATIO_LONG_NAME = "pileup-detection-bad-read-tolerance";
     public static final String PILEUP_DETECTION_PROPER_PAIR_READ_BADNESS_LONG_NAME = "pileup-detection-proper-pair-read-badness";
@@ -57,10 +56,6 @@ public final class PileupDetectionArgumentCollection {
     @Argument(fullName= "artifical-haplotype-filtering-kmer-size", doc = "Pileup Detection: Controls what size to kmerize reads to in order to select best supported artificial haplotypes", optional = true)
     public int filteringKmerSize = 10;
 
-
-
-
-
     /**
      * Percentage of reads required to support the alt for a variant to be considered
      */
@@ -71,17 +66,13 @@ public final class PileupDetectionArgumentCollection {
     @Argument(fullName= PILEUP_DETECTION_INDEL_THRESHOLD, doc = "Pileup Detection: Percentage of alt supporting reads in order to consider alt indel", optional = true)
     public double indelThreshold = 0.5;
 
-
     @Hidden
     @Argument(fullName= PILEUP_DETECTION_ABSOLUTE_ALT_DEPTH, doc = "Pileup Detection: Absolute number of alt reads necessary to be included in pileup events", optional = true)
     public double pileupAbsoluteDepth = 0;
     @Hidden
     @Argument(fullName= PILEUP_DETECTION_INDEL_SNP_BLOCKING_RANGE, doc = "Pileup Detection: Filters out pileup snps within this many bases of an assembled indel", optional = true)
     public int snpAdajacentToAssemblyIndel = 5;
 
-
-
-
     /**
      * Arguments related to the "bad read filtering" where alleles that are supported primarily by reads that fail at least one of a number of heuristics will be filtered out
      */

diff --git a/...dinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtilsUnitTest.java b/...dinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtilsUnitTest.java
@@ -1391,7 +1391,8 @@ public Object[][] filterPileupHaplotypesDataProvider() {
         final Haplotype hapD = new Haplotype("ACCTGAA".getBytes());
         final Haplotype hapF = new Haplotype("GAAGAAG".getBytes()); // testing repeated kmers
 
-        Map<Kmer, Integer> flatSupportAllKmers = new HashMap<Kmer, Integer>() { private static final long serialVersionUID = 0L; {
+        Map<Kmer, Integer> flatSupportAllKmers = new HashMap<Kmer, Integer>() {
+            private static final long serialVersionUID = 0L; {
             put(new Kmer("ACC"), 1);
             put(new Kmer("CCT"), 1);
             put(new Kmer("CTG"), 1);
@@ -1405,7 +1406,8 @@ public Object[][] filterPileupHaplotypesDataProvider() {
             put(new Kmer("AAG"), 1);
         }};
 
-        Map<Kmer, Integer> hapDKmersHighSupport = new HashMap<Kmer, Integer>() { private static final long serialVersionUID = 0L;{
+        Map<Kmer, Integer> hapDKmersHighSupport = new HashMap<Kmer, Integer>() {
+            private static final long serialVersionUID = 0L;{
             put(new Kmer("ACC"), 10);
             put(new Kmer("CCT"), 10);
             put(new Kmer("CTG"), 10);
@@ -1419,15 +1421,17 @@ public Object[][] filterPileupHaplotypesDataProvider() {
             put(new Kmer("AAG"), 1);
         }};
 
-        Map<Kmer, Integer> hapDKmers = new HashMap<Kmer, Integer>() { private static final long serialVersionUID = 0L; {
+        Map<Kmer, Integer> hapDKmers = new HashMap<Kmer, Integer>() {
+            private static final long serialVersionUID = 0L; {
             put(new Kmer("ACC"), 10);
             put(new Kmer("CCT"), 10);
             put(new Kmer("CTG"), 10);
             put(new Kmer("TGA"), 10);
             put(new Kmer("GAA"), 10);
         }};
 
-        Map<Kmer, Integer> hapFRepeatedKmers = new HashMap<Kmer, Integer>() { private static final long serialVersionUID = 0L; {
+        Map<Kmer, Integer> hapFRepeatedKmers = new HashMap<Kmer, Integer>() {
+            private static final long serialVersionUID = 0L; {
             put(new Kmer("GAA"), 1);
         }};
 
@@ -1439,7 +1443,7 @@ public Object[][] filterPileupHaplotypesDataProvider() {
                 new Object[]{Arrays.asList(hapA,hapB,hapC,hapD),flatSupportAllKmers,2,3,Arrays.asList(hapA,hapB)},
                 new Object[]{Arrays.asList(hapA,hapB,hapC,hapD),flatSupportAllKmers,3,3,Arrays.asList(hapA,hapB,hapC)},
 
-                // Repetative kmers in hapF don't get double counted
+                // Repetitive kmers in hapF don't get double counted
                 new Object[]{Arrays.asList(hapA,hapB,hapD,hapF),hapFRepeatedKmers,2,3,Arrays.asList(hapF,hapD)},
                 new Object[]{Arrays.asList(hapA,hapB,hapD,hapF),hapFRepeatedKmers,1,3,Arrays.asList(hapD)}, //currently repeated kmers only count as singular evidence