From 4505f08f536449c5f4a8c57b219c0143bcf482a8 Mon Sep 17 00:00:00 2001
From: Daniel Cameron <daniel.l.cameron@gmail.com>
Date: Mon, 21 May 2018 15:07:09 +1000
Subject: [PATCH] Updated VF and BCF to incorporate #114

---
 pom.xml                                       |  2 +-
 .../idsv/StructuralVariationCallBuilder.java  | 19 ++++++++++++++++---
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index b0339ee38..d37234738 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<groupId>au.edu.wehi</groupId>
 	<artifactId>gridss</artifactId>
 	<packaging>jar</packaging>
-	<version>1.7.0-gridss</version>
+	<version>1.7.1-gridss-SNAPSHOT</version>
 	<name>gridss</name>
 	<url>https://github.com/PapenfussLab/gridss</url>
 	<properties>
diff --git a/src/main/java/au/edu/wehi/idsv/StructuralVariationCallBuilder.java b/src/main/java/au/edu/wehi/idsv/StructuralVariationCallBuilder.java
index 5ac5adbc8..1146c4963 100644
--- a/src/main/java/au/edu/wehi/idsv/StructuralVariationCallBuilder.java
+++ b/src/main/java/au/edu/wehi/idsv/StructuralVariationCallBuilder.java
@@ -11,6 +11,7 @@
 import java.util.stream.Stream;
 
 import com.google.common.collect.ComparisonChain;
+import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Ordering;
 import com.google.common.collect.Range;
 import com.google.common.collect.RangeSet;
@@ -277,17 +278,29 @@ public VariantContextDirectedEvidence make() {
 					.mapToInt(ass -> ass.getCategorySupportBreakdown().get(category) ? new AssemblyAttributes(ass.getSAMRecord()).getAssemblySupportCountReadPair(category) : 0)
 					.sum();
 			Set<String> bpfrags = supportingBreakpoint.stream()
-					.map(e -> e.getOriginatingFragmentID(category))
+					.map(e -> {
+						if (AssemblyAttributes.isAssembly(e)) {
+							SingleReadEvidence ass = (SingleReadEvidence)e; 
+							return ass.getCategorySupportBreakdown().get(category) ? e.getOriginatingFragmentID(category) : ImmutableList.<String>of();
+						}
+						return e.getOriginatingFragmentID(category); 
+					})
 					.flatMap(x -> x.stream())
 					.collect(Collectors.toSet());
 			supportingBreakpointFragments[category] = bpfrags.size();
 			Set<String> befrags = supportingBreakend.stream()
-					.map(e -> e.getOriginatingFragmentID(category))
+					.map(e -> {
+						if (AssemblyAttributes.isAssembly(e)) {
+							SingleReadEvidence ass = (SingleReadEvidence)e; 
+							return ass.getCategorySupportBreakdown().get(category) ? e.getOriginatingFragmentID(category) : ImmutableList.<String>of();
+						}
+						return e.getOriginatingFragmentID(category); 
+					})
 					.flatMap(x -> x.stream())
 					.collect(Collectors.toSet());
 			befrags.removeAll(bpfrags);
 			supportingBreakendFragments[category] = befrags.size();
-					
+			
 			genotypeBuilder.get(category).attribute(VcfFormatAttributes.BREAKPOINT_ASSEMBLY_READ_COUNT.attribute(), asr[category]);
 			genotypeBuilder.get(category).attribute(VcfFormatAttributes.BREAKPOINT_ASSEMBLY_READPAIR_COUNT.attribute(), asrp[category]);
 			genotypeBuilder.get(category).attribute(VcfFormatAttributes.BREAKEND_ASSEMBLY_READ_COUNT.attribute(), basr[category]);