Fixed regression bug in findBreakpointOverlaps()

Author: Daniel Cameron

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: StructuralVariantAnnotation
 Type: Package
 Title: VariantionAnnoration for Structural Variants
-Version: 0.7.2
+Version: 0.7.3
 Date: 2018-01-25
 Author: Daniel Cameron
 Maintainer: Daniel Cameron <daniel.l.cameron@gmail.com>

R/BreakpointGRanges.R

@@ -33,7 +33,9 @@ partner <- function(gr) {
 findBreakpointOverlaps <- function(query, subject, maxgap=-1L, minoverlap=0L, ignore.strand=FALSE, sizemargin=0.25, restrictMarginToSizeMultiple=0.5) {
 	hits <- dplyr::bind_rows(
 		as.data.frame(findOverlaps(query, subject, maxgap=maxgap, minoverlap=minoverlap, type="any", select="all", ignore.strand=ignore.strand), row.names=NULL),
-		as.data.frame(findOverlaps(query, subject, maxgap=maxgap, minoverlap=minoverlap, type="any", select="all", ignore.strand=ignore.strand), row.names=NULL))
+		as.data.frame(findOverlaps(partner(query), partner(subject), maxgap=maxgap, minoverlap=minoverlap, type="any", select="all", ignore.strand=ignore.strand), row.names=NULL))
+	#as.data.frame(findOverlaps(partner(query), partner(subject), maxgap=maxgap, minoverlap=minoverlap, type="any", select="all", ignore.strand=ignore.strand), row.names=NULL))
+
 	# we now want to do:
 	# hits <- hits[duplicated(hits),] # both breakends match
 	# but for large hit sets (such as focal false positive loci) we run out of memory (>32GB)

tests/testthat/test-BreakpointGRanges.R

@@ -36,11 +36,10 @@ test_that(".constrict", {
 	expect_equal(start(gr), c(1, 16571))
 })
 
-
+justHits <- function(df) {
+	return(data.frame(queryHits=df$queryHits, subjectHits=df$subjectHits))
+}
 test_that("findBreakpointOverlaps", {
-	justHits <- function(df) {
-		return(data.frame(queryHits=df$queryHits, subjectHits=df$subjectHits))
-	}
 	expect_equal(justHits(findBreakpointOverlaps(breakpointRanges(.testrecord(c(
 			"chr1	100000	a	N	N[chr1:100100[	.	.	SVTYPE=BND;PARID=b",
 			"chr1	100100	b	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=a",
@@ -84,6 +83,13 @@ test_that("findBreakpointOverlaps", {
 		maxgap=1)),
 		data.frame(queryHits=c(1,2), subjectHits=c(2,1)))
 })
+test_that("findBreakpointOverlaps_match_both_sides", {
+	gr1 = GRanges(seqnames="1", ranges=IRanges(start=c(1, 100), width=1), strand="+", partner=c("2", "1"))
+	names(gr1) = c("1", "2")
+	gr2 = GRanges(seqnames="1", ranges=IRanges(start=c(100, 100), width=1),  strand="+", partner=c("2", "1"))
+	names(gr2) = c("1", "2")
+	expect_equal(nrow(findBreakpointOverlaps(gr1, gr2, sizemargin=NULL)), 0)
+})
 
 test_that("findBreakpointOverlaps: delly vs truth", {
 	grdelly <- breakpointRanges(.testrecord(c(