Fixed GatherTranches -- gathered tranches should be closer to target truth sensitivity in the lower range (~90%) now (#4313)

Author: ldgauthier

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/GatherTranches.java

@@ -63,7 +63,7 @@ protected Object doWork() {
         }
 
         //use a data structure to hold the tranches from each scatter shard in a format that's easy to merge
-        final Map<Double, List<VQSLODTranche>> scatteredTranches = new HashMap<>();
+        final TreeMap<Double, List<VQSLODTranche>> scatteredTranches = new TreeMap<>();
         for (final File trancheFile : inputReports) {
             try {
                 for (final VQSLODTranche currentTranche : VQSLODTranche.readTranches(trancheFile)) {

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VQSLODTranche.java

@@ -130,12 +130,12 @@ public static List<VQSLODTranche> readTranches(final File f) throws IOException{
         return tranches;
     }
 
-    public static List<TruthSensitivityTranche> mergeAndConvertTranches(final Map<Double, List<VQSLODTranche>> scatteredTranches, final List<Double> tsLevels, final VariantRecalibratorArgumentCollection.Mode mode) {
+    public static List<TruthSensitivityTranche> mergeAndConvertTranches(final TreeMap<Double, List<VQSLODTranche>> scatteredTranches, final List<Double> tsLevels, final VariantRecalibratorArgumentCollection.Mode mode) {
         List<VQSLODTranche> mergedTranches = new ArrayList<>();
         List<TruthSensitivityTranche> gatheredTranches = new ArrayList<>();
 
         //make a list of merged tranches of the same length
-        for (final Double VQSLODlevel : scatteredTranches.keySet()) {
+        for (final Double VQSLODlevel : scatteredTranches.descendingKeySet()) {
             mergedTranches.add(mergeAndConvertTranches(scatteredTranches.get(VQSLODlevel),mode));
         }
 

src/test/resources/large/VQSR/expected/snpTranches.gathered.txt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:84435fbcadecb6904210371229fb373dd76092ccb91cec3255a189df48b423f7
-size 568
+oid sha256:e2c27cfe8f79a1cc8f796a889884472d5fca489e25ee4cb36ac811a771edad81
+size 569