From 962820224b5d49ef78eec02327a534f563ce1810 Mon Sep 17 00:00:00 2001
From: Daniel Cameron <cameron.d@wehi.edu.au>
Date: Tue, 29 Aug 2017 17:04:46 +1000
Subject: [PATCH] Excluding single binversion-like breakpoints from minSize
 check as the event size is not known from just the single breakpoint

---
 pom.xml                                       |  2 +-
 .../VariantContextDirectedBreakpoint.java     | 23 ++++++++++++++++++-
 .../VariantContextDirectedBreakpointTest.java |  7 ++++--
 3 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index 557c98756..3d4c76d6a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<groupId>au.edu.wehi</groupId>
 	<artifactId>gridss</artifactId>
 	<packaging>jar</packaging>
-	<version>1.4.2</version>
+	<version>1.4.3</version>
 	<name>gridss</name>
 	<url>https://github.com/PapenfussLab/gridss</url>
 	<properties>
diff --git a/src/main/java/au/edu/wehi/idsv/VariantContextDirectedBreakpoint.java b/src/main/java/au/edu/wehi/idsv/VariantContextDirectedBreakpoint.java
index d9080b090..5bce4cb62 100644
--- a/src/main/java/au/edu/wehi/idsv/VariantContextDirectedBreakpoint.java
+++ b/src/main/java/au/edu/wehi/idsv/VariantContextDirectedBreakpoint.java
@@ -24,17 +24,38 @@ public VariantContextDirectedBreakpoint(GenomicProcessingContext processContext,
 	public Integer getEventSize() {
 		BreakendSummary low = getBreakendSummary().lowBreakend();
 		BreakendSummary high = getBreakendSummary().highBreakend();
-		if (low.referenceIndex != high.referenceIndex) return null;
+		if (low.referenceIndex != high.referenceIndex) {
+			return null;
+		}
 		int sizeAdjustment = -1; // assume indel
 		if (low.direction == high.direction) {
 			// inversion
 			sizeAdjustment = 0;
+			// requires a second breakpoint to explain - we're not going to assume this breakpoint exists
+			// as the event could be a large fold-back inversion
+			return null; 
 		} else if (low.direction == BreakendDirection.Backward && high.direction == BreakendDirection.Forward) {
 			// tandem dup
 			sizeAdjustment = 1;
 		}
 		return high.nominal - low.nominal + getUntemplatedSequence().length() + sizeAdjustment; 
 	}
+	/**
+	 * Size of indel event. 
+	 * @return size of indel inferred by breakpoint, null otherwise
+	 */
+	public Integer getIndelSize() {
+		BreakendSummary low = getBreakendSummary().lowBreakend();
+		BreakendSummary high = getBreakendSummary().highBreakend();
+		if (low.direction == high.direction) {
+			// inversion
+			return null;
+		} else if (low.direction == BreakendDirection.Backward && high.direction == BreakendDirection.Forward) {
+			// tandem dup
+			return null;
+		}
+		return getEventSize(); 
+	}
 	@Override
 	public BreakpointSummary getBreakendSummary() {
 		return (BreakpointSummary)super.getBreakendSummary();
diff --git a/src/test/java/au/edu/wehi/idsv/VariantContextDirectedBreakpointTest.java b/src/test/java/au/edu/wehi/idsv/VariantContextDirectedBreakpointTest.java
index f138fca50..719718a2b 100644
--- a/src/test/java/au/edu/wehi/idsv/VariantContextDirectedBreakpointTest.java
+++ b/src/test/java/au/edu/wehi/idsv/VariantContextDirectedBreakpointTest.java
@@ -77,9 +77,12 @@ public void getEventSize_INSDEL() {
 	public void getEventSize_DUP() {
 		assertEquals(4, (int)BP("dup", new BreakpointSummary(0, FWD, 10, 0, BWD, 7)).getEventSize());
 	}
+	/**
+	 * inversion have two breakpoints - we don't know the event size unless we actually have both of them
+	 */
 	@Test
 	public void getEventSize_INV() {
-		assertEquals(4, (int)BP("inv", new BreakpointSummary(0, FWD, 6, 0, FWD, 10)).getEventSize());
-		assertEquals(4, (int)BP("inv", new BreakpointSummary(0, BWD, 11, 0, BWD, 7)).getEventSize());
+		assertEquals(null, BP("inv", new BreakpointSummary(0, FWD, 6, 0, FWD, 10)).getEventSize());
+		assertEquals(null, BP("inv", new BreakpointSummary(0, BWD, 11, 0, BWD, 7)).getEventSize());
 	}
 }