#213 Excluding local assembly anchoring from SC calculation; added ASC

src/main/java/au/edu/wehi/idsv/StructuralVariationCallBuilder.java

@@ -277,10 +277,17 @@ private void updateNominalCallPosition() {
 		supportingSR.stream().flatMap(l -> l.stream()).forEach(e -> processAnchor(allAnchoredBases, e.getSAMRecord()));
 		supportingIndel.stream().flatMap(l -> l.stream()).forEach(e -> processAnchor(allAnchoredBases, e.getSAMRecord()));
 		supportingDP.stream().flatMap(l -> l.stream()).forEach(e -> processAnchor(allAnchoredBases, e.getLocalledMappedRead()));
-		supportingAS.stream().forEach(e -> processAnchor(allAnchoredBases, e.getSAMRecord()));
+		//supportingAS.stream().forEach(e -> processAnchor(allAnchoredBases, e.getSAMRecord()));
 		supportingRAS.stream().forEach(e -> processAnchor(allAnchoredBases, e.getSAMRecord()));
 		supportingCAS.stream().forEach(e -> processAnchor(allAnchoredBases, e.getSAMRecord()));
 		attribute(VcfInfoAttributes.SUPPORT_CIGAR, makeCigar(allAnchoredBases, nominalPosition).toString());
+		RangeSet<Integer> assemblyAnchoredBases = TreeRangeSet.create();
+		// TODO: implement https://github.com/PapenfussLab/gridss/issues/213 so we can include local assemblies
+		//supportingAS.stream().forEach(e -> processAnchor(allAnchoredBases, e.getSAMRecord()));
+		supportingRAS.stream().forEach(e -> processAnchor(assemblyAnchoredBases, e.getSAMRecord()));
+		supportingCAS.stream().forEach(e -> processAnchor(assemblyAnchoredBases, e.getSAMRecord()));
+		attribute(VcfInfoAttributes.ASSEMBLY_SUPPORT_CIGAR, makeCigar(assemblyAnchoredBases, nominalPosition).toString());
+
 	}
 
 	private void updateAssemblySupportTracking() {

src/main/java/au/edu/wehi/idsv/configuration/VariantCallingConfiguration.java

@@ -170,8 +170,8 @@ public VariantContextDirectedEvidence applyConfidenceFilter(ProcessingContext pr
 				filters.add(VcfFilter.NO_ASSEMBLY.filter());
 			} else if (v.getBreakpointEvidenceCountLocalAssembly() == 0 || v.getBreakpointEvidenceCountRemoteAssembly() == 0) {
 				filters.add(VcfFilter.SINGLE_ASSEMBLY.filter());
-			} else if (v.getBreakpointEvidenceCountLocalAssembly() + v.getBreakpointEvidenceCountRemoteAssembly() > 0 &&
-					v.getBreakpointEvidenceCountReadPair() + v.getBreakpointEvidenceCountSoftClip() == 0) {
+			} else if (v.getBreakpointEvidenceCountLocalAssembly() + v.getBreakpointEvidenceCountRemoteAssembly() + v.getBreakpointEvidenceCountCompoundAssembly() > 0 &&
+					v.getBreakpointEvidenceCountReadPair() + v.getBreakpointEvidenceCountSoftClip() + v.getBreakpointEvidenceCountIndel() == 0) {
 				filters.add(VcfFilter.ASSEMBLY_ONLY.filter());
 			}
 			if (variant.getPhredScaledQual() < processContext.getVariantCallingParameters().breakpointLowQuality) {

src/main/java/au/edu/wehi/idsv/vcf/VcfInfoAttributes.java

@@ -60,7 +60,8 @@ public enum VcfInfoAttributes {
 	SUPPORT_INTERVAL ("SI", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Support interval offsets from breakend position in which at least one supporting read/read pair/assembly is mapped."),
 	REMOTE_SUPPORT_INTERVAL ("RSI", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Support interval offsets of partner breakend."),
 	INEXACT_HOMPOS ("IHOMPOS", 2, VCFHeaderLineType.Integer, "Position of inexact homology"),
-	SUPPORT_CIGAR ("SC", 1, VCFHeaderLineType.String, "CIGAR for displaying anchoring alignment of any contributing evidence and microhomologies."),
+	SUPPORT_CIGAR ("SC", 1, VCFHeaderLineType.String, "CIGAR for displaying anchoring alignment of any contributing evidence and microhomologies. Local assemblies are excluded due to https://github.com/PapenfussLab/gridss/issues/213"),
+	ASSEMBLY_SUPPORT_CIGAR ("ASC", 1, VCFHeaderLineType.String, "CIGAR encoding assembly contig anchoring alignments. Local assemblies are excluded due to https://github.com/PapenfussLab/gridss/issues/213."),
 	BREAKEND_ASSEMBLY_ID ("BEID", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Identifiers of assemblies supporting the variant."),
 	BREAKEND_ASSEMBLY_ID_LOCAL_CONTIG_OFFSET ("BEIDL", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Local chimeric alignment offset of corresponding BEID assembly."),
 	BREAKEND_ASSEMBLY_ID_REMOTE_CONTIG_OFFSET ("BEIDH", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Remote chimeric alignment offset of corresponding BEID assembly."),

src/test/java/au/edu/wehi/idsv/StructuralVariationCallBuilderTest.java

@@ -728,6 +728,25 @@ public void anchor_cigar_should_use_local_coordinates() {
 		assertEquals("9M1X", vc.getAttribute(VcfInfoAttributes.SUPPORT_CIGAR.attribute()));
 	}
 	@Test
+	public void assembly_anchor_cigar_should_use_only_remote_assemblies() {
+		ProcessingContext pc = getContext();
+		AssemblyEvidenceSource aes = AES(pc);
+		StructuralVariationCallBuilder builder = new StructuralVariationCallBuilder(pc, (VariantContextDirectedEvidence)new IdsvVariantContextBuilder(getContext()) {{
+			breakpoint(new BreakpointSummary(0, FWD, 100, 1, BWD, 200), "");
+			phredScore(10);
+		}}.make());
+		List<DirectedEvidence> support = Lists.<DirectedEvidence>newArrayList(
+				SR(Read(1, 200, "3S7M"), Read(0, 98, "3M7S"))
+		);
+		SAMRecord ass = AssemblyFactory.createAnchoredBreakend(pc, aes, new SequentialIdGenerator("asm"), BWD, support, fullSupport(support), 1, 200, 7, B("NNNNNNNNNN"), B("NNNNNNNNNN"));
+		SAMRecord beass = withMapq(44, Read(0, 98, "3M"))[0];
+		incorporateRealignment(AES(), ass, ImmutableList.of(beass));
+
+		builder.addEvidence(SingleReadEvidence.createEvidence(AES(), 1, beass).get(0));
+		VariantContextDirectedEvidence vc = builder.make();
+		assertEquals("2M1X", vc.getAttribute(VcfInfoAttributes.ASSEMBLY_SUPPORT_CIGAR.attribute()));
+	}
+	@Test
 	@Ignore("The assembler doesn't know which orientation it was assembling.")
 	public void spanning_assemblies_should_use_original_parent_assembly_direction_to_determine_local_remote_status() {
 		IndelEvidence r = IE(withMapq(40, Read(2, 90, "10M1I10M"))[0]);