Make code determine the collapsing automatically

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java

@@ -337,7 +337,8 @@ public SWParameters getReadToHaplotypeSWParameters() {
 
     @Hidden
     @Advanced
-    @Argument(fullName=FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, doc="Collapse reference regions with >Nhmer during assembly, normal value when used is 12", optional = true)
+    @Argument(fullName=FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, doc="Collapse reference regions with >Nhmer during assembly, normal value when used is 12, " +
+            "-1 means - determine automatically from mc tag in the reads, 0 - disable", optional = true)
     public int flowAssemblyCollapseHKerSize = 0;
 
     @Advanced

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java

@@ -4,6 +4,7 @@
 import htsjdk.samtools.Cigar;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileWriter;
+import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.util.Locatable;
 import htsjdk.variant.variantcontext.*;
@@ -52,6 +53,7 @@
 public final class AssemblyBasedCallerUtils {
 
     public static final int REFERENCE_PADDING_FOR_ASSEMBLY = 500;
+    public static final int DETERMINE_COLLAPSE_THRESHOLD = -1;
     public static final int NUM_HAPLOTYPES_TO_INJECT_FORCE_CALLING_ALLELES_INTO = 5;
     public static final String SUPPORTED_ALLELES_TAG="XA";
     public static final String CALLABLE_REGION_TAG = "CR";
@@ -363,8 +365,12 @@ public static AssemblyResultSet assembleReads(final AssemblyRegion region,
         final SWParameters haplotypeToReferenceSWParameters = argumentCollection.getHaplotypeToReferenceSWParameters();
 
         // establish reference mapper, if needed
-        final LongHomopolymerHaplotypeCollapsingEngine haplotypeCollapsing = (argumentCollection.flowAssemblyCollapseHKerSize > 0 && LongHomopolymerHaplotypeCollapsingEngine.needsCollapsing(refHaplotype.getBases(), argumentCollection.flowAssemblyCollapseHKerSize, logger))
-                                            ? new LongHomopolymerHaplotypeCollapsingEngine(argumentCollection.flowAssemblyCollapseHKerSize, argumentCollection.flowAssemblyCollapsePartialMode, fullReferenceWithPadding,
+        int collapseHmerSize = argumentCollection.flowAssemblyCollapseHKerSize;
+        if (collapseHmerSize == DETERMINE_COLLAPSE_THRESHOLD){
+            collapseHmerSize = AssemblyBasedCallerUtils.determineFlowAssemblyColapseHmer(header);
+        }
+        final LongHomopolymerHaplotypeCollapsingEngine haplotypeCollapsing = ( collapseHmerSize > 0 && LongHomopolymerHaplotypeCollapsingEngine.needsCollapsing(refHaplotype.getBases(), collapseHmerSize, logger))
+                                            ? new LongHomopolymerHaplotypeCollapsingEngine(collapseHmerSize, argumentCollection.flowAssemblyCollapsePartialMode, fullReferenceWithPadding,
                 paddedReferenceLoc, logger, argumentCollection.assemblerArgs.debugAssembly, aligner, argumentCollection.getHaplotypeToReferenceSWParameters())
                                             : null;
         if ( haplotypeCollapsing != null ) {
@@ -411,6 +417,18 @@ public static AssemblyResultSet assembleReads(final AssemblyRegion region,
         }
     }
 
+    private static int determineFlowAssemblyColapseHmer(SAMFileHeader readsHeader) {
+        int result = 0;
+        List<SAMReadGroupRecord> rgr = readsHeader.getReadGroups();
+        for (SAMReadGroupRecord rg : rgr) {
+            FlowBasedReadUtils.ReadGroupInfo rgi = new FlowBasedReadUtils.ReadGroupInfo(rg);
+            if (rgi.maxClass >= result) {
+                result = rgi.maxClass;
+            }
+        }
+        return result;
+    }
+
     /**
      * Handle pileup detected alternate alleles.
      */
@@ -1217,4 +1235,5 @@ private static GATKRead revertSoftClippedBases(GATKRead inputRead){
         result.setAttribute(ReferenceConfidenceModel.ORIGINAL_SOFTCLIP_END_TAG, softEnd);
         return result;
     }
+
 }

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java

@@ -264,7 +264,7 @@ public enum FlowMode {
                 MIN_BASE_QUALITY_SCORE_SHORT_NAME, "0",
                 FILTER_ALLELES, "true",
                 FILTER_ALLELES_SOR_THRESHOLD, "3",
-                FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, "20",
+                FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, String.valueOf(AssemblyBasedCallerUtils.DETERMINE_COLLAPSE_THRESHOLD),
                 OVERRIDE_FRAGMENT_SOFTCLIP_CHECK_LONG_NAME, "true",
                 FlowBasedAlignmentArgumentCollection.FLOW_LIKELIHOOD_PARALLEL_THREADS_LONG_NAME, "2",
                 FlowBasedAlignmentArgumentCollection.FLOW_LIKELIHOOD_OPTIMIZED_COMP_LONG_NAME, "true",

src/main/java/org/broadinstitute/hellbender/utils/read/FlowBasedReadUtils.java

@@ -29,7 +29,7 @@ static public class ReadGroupInfo {
 
         private String  reversedFlowOrder = null;
 
-        ReadGroupInfo(final SAMReadGroupRecord readGroup) {
+        public ReadGroupInfo(final SAMReadGroupRecord readGroup) {
 
             Utils.nonNull(readGroup);
             this.flowOrder = readGroup.getFlowOrder();