tweak bwa to allow gappier alignments in local assemblies

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/StructuralVariationDiscoveryArgumentCollection.java

@@ -121,6 +121,9 @@ public static class FindBreakpointEvidenceSparkArgumentCollection implements Ser
         @Argument(doc = "Traverse assembly graph and produce contigs for all paths.", fullName = "expand-assembly-graph")
         public boolean expandAssemblyGraph = true;
 
+        @Advanced @Argument(doc = "ZDropoff (see Bwa mem manual) for contig alignment.", fullName = "z-dropoff")
+        public int zDropoff = 20;
+
         // --------- locations ----------
 
         @Argument(doc = "bwa-mem index image file", fullName = "aligner-index-image")

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/FermiLiteAssemblyHandler.java

@@ -29,18 +29,20 @@ public final class FermiLiteAssemblyHandler implements FindBreakpointEvidenceSpa
     private final boolean popVariantBubbles;
     private final boolean removeShadowedContigs;
     private final boolean expandAssemblyGraph;
+    private final int zDropoff;
 
     public FermiLiteAssemblyHandler( final String alignerIndexFile, final int maxFastqSize,
                                      final String fastqDir, final boolean writeGFAs,
                                      final boolean popVariantBubbles, final boolean removeShadowedContigs,
-                                     final boolean expandAssemblyGraph ) {
+                                     final boolean expandAssemblyGraph, final int zDropoff ) {
         this.alignerIndexFile = alignerIndexFile;
         this.maxFastqSize = maxFastqSize;
         this.fastqDir = fastqDir;
         this.writeGFAs = writeGFAs;
         this.popVariantBubbles = popVariantBubbles;
         this.removeShadowedContigs = removeShadowedContigs;
         this.expandAssemblyGraph = expandAssemblyGraph;
+        this.zDropoff = zDropoff;
     }
 
     /** This method creates an assembly with FermiLite, and uses the graph information returned by that
@@ -99,6 +101,7 @@ public AlignedAssemblyOrExcuse apply( final Tuple2<Integer, List<SVFastqUtils.Fa
         // align the assembled contigs to the genomic reference
         try ( final BwaMemAligner aligner = new BwaMemAligner(BwaMemIndexCache.getInstance(alignerIndexFile)) ) {
             aligner.setIntraCtgOptions();
+            aligner.setZDropOption(zDropoff);
             final List<byte[]> sequences =
                     assembly.getContigs().stream()
                             .map(Contig::getSequence)

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/FindBreakpointEvidenceSpark.java

@@ -179,7 +179,7 @@ public static AssembledEvidenceResults gatherEvidenceAndWriteContigSamFile(
                 new FermiLiteAssemblyHandler(params.alignerIndexImageFile, params.maxFASTQSize,
                                                 params.fastqDir, params.writeGFAs,
                                                 params.popVariantBubbles, params.removeShadowedContigs,
-                                                params.expandAssemblyGraph);
+                                                params.expandAssemblyGraph, params.zDropoff);
         alignedAssemblyOrExcuseList.addAll(
                 handleAssemblies(ctx, qNamesMultiMap, unfilteredReads, filter, intervals.size(),
                         params.includeMappingLocation, fermiLiteAssemblyHandler));