Description: Skip test requiring BSgenome.Hsapiens.UCSC.hg19
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 14 Sep 2021 21:16:27 +0200

--- a/tests/testthat/test-BreakpointGRanges.R
+++ b/tests/testthat/test-BreakpointGRanges.R
@@ -19,444 +19,4 @@ test_that("bedpe2breakpointgr creates un
 test_that("partner fails if missing mate", {
     expect_error(partner(breakpointRanges(breakend)[1,]))
 })
-requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly=FALSE)
-hg19 <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
 
-test_that(".constrict", {
-	expect_equal(IRanges::width(.constrict(breakpointRanges(breakend))), rep(1, length(breakpointRanges(breakend))))
-	expect_equal(start(.constrict(breakpointRanges(.testrecord(c(
-		"chr1	100000	a	N	N[chr1:100100[	.	.	SVTYPE=BND;CIPOS=0,1;PARID=b",
-		"chr1	100100	b	N	]chr1:100000]N	.	.	SVTYPE=BND;CIPOS=0,1;PARID=a",
-		"chr1	100000	c	N	N]chr1:100100]	.	.	SVTYPE=BND;CIPOS=0,1;PARID=d",
-		"chr1	100100	d	N	N]chr1:100000]	.	.	SVTYPE=BND;CIPOS=0,1;PARID=c"
-		))))), c(100000, 100100, # not 100001, 100101
-			100000, 100101))
-	gr <- .constrict(breakpointRanges(.testrecord(c(
-		"chrM	1	a	G	]chrM:16571]G	.	.	SVTYPE=BND;PARID=b;CIPOS=-10,-5",
-		"chrM	16571	b	G	G[chrM:1[	.	.	SVTYPE=BND;PARID=a;CIPOS=5,10"
-		))), hg19)
-	expect_equal(start(gr), c(1, 16571))
-})
-test_that("findBreakpointOverlaps", {
-	expect_equal(as.data.frame(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",
-			"chr1	100000	c	N	N[chr1:100200[	.	.	SVTYPE=BND;PARID=d",
-			"chr1	100200	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c"))),
-		breakpointRanges(.testrecord(c(
-			"chr1	100000	c	N	N[chr1:100200[	.	.	SVTYPE=BND;PARID=d",
-			"chr1	100200	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c"))))),
-		data.frame(queryHits=c(3,4), subjectHits=c(1,2)))
-
-	expect_equal(as.data.frame(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",
-			"chr1	100000	c	N	N[chr1:100200[	.	.	SVTYPE=BND;PARID=d",
-			"chr1	100200	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c"))),
-		breakpointRanges(.testrecord(c(
-			"chr1	100000	c	N	N[chr1:100200[	.	.	SVTYPE=BND;PARID=d",
-			"chr1	100200	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c"))),
-		maxgap=2000, sizemargin=NULL)),
-		data.frame(queryHits=c(1,2,3,4), subjectHits=c(1,2,1,2)))
-
-	expect_equal(as.data.frame(findBreakpointOverlaps(breakpointRanges(.testrecord(c(
-			"chr1	1	a	N	N[chr1:100100[	.	.	SVTYPE=BND;CIPOS=0,100000;PARID=b",
-			"chr1	100100	b	N	]chr1:1]N	.	.	SVTYPE=BND;PARID=a"))),
-		breakpointRanges(.testrecord(c(
-			"chr1	100000	c	N	N[chr1:100100[	.	.	SVTYPE=BND;PARID=d",
-			"chr1	100100	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c"))))),
-		data.frame(queryHits=c(1,2), subjectHits=c(1,2)))
-	expect_equal(as.data.frame(findBreakpointOverlaps(breakpointRanges(.testrecord(c(
-			"chr1	10000	a	N	<DEL>	.	.	SVTYPE=DEL;SVLEN=-1000"))),
-		breakpointRanges(.testrecord(c(
-			"chr1	10000	c	N	N[chr1:11000[	.	.	SVTYPE=BND;PARID=d",
-			"chr1	11000	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c"))),
-		maxgap=1)),
-		data.frame(queryHits=c(1,2), subjectHits=c(1,2)))
-	expect_equal(as.data.frame(findBreakpointOverlaps(breakpointRanges(.testrecord(c(
-			"chr1	10000	a	N	<DEL>	.	.	SVTYPE=DEL;SVLEN=-1000"))),
-		breakpointRanges(.testrecord(c(
-			"chr1	11000	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c",
-			"chr1	10000	c	N	N[chr1:11000[	.	.	SVTYPE=BND;PARID=d"))),
-		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(as.data.frame(findBreakpointOverlaps(gr1, gr2, sizemargin=NULL))), 0)
-})
-
-test_that("findBreakpointOverlaps: delly vs truth", {
-	grdelly <- breakpointRanges(.testrecord(c(
-		"chr12	6905246	DEL00000292	N	<DEL>	.	PASS	PRECISE;CIEND=-52,52;CIPOS=-52,52;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.6.8;CHR2=chr12;END=100419669;CT=3to5;INSLEN=0;PE=28;MAPQ=34;SR=30;SRQ=1;CONSENSUS=GTGCATACATTTCAGTGACCCGTTTTAGAAACAGAATTAATATGGTGAATAGAGAAAGAAGAAATCAGTGACTTTGGCCAGGCACAGTAGCTCACATCTGTAATCCCAGCACTTTGGGAGGCTGAGACAGTTGGTTGCTTGAGCCCAGGAGT"
-		)))
-	grtruth <- breakpointRanges(.testrecord(c(
-		"chr12	6905247	truth_8545_o	C	C[chr12:100419669[	.	.	EVENT=truth_8545_;MATEID=truth_8545_h;PARID=truth_8545_h;SVTYPE=BND",
-		"chr12	100419669	truth_8545_h	G	]chr12:6905247]g	.	.	EVENT=truth_8545_;MATEID=truth_8545_o;PARID=truth_8545_o;SVTYPE=BND"
-		)))
-	hits <- findBreakpointOverlaps(grdelly, grtruth, maxgap=200, ignore.strand=TRUE)
-	expect_equal(2, nrow(as.data.frame(hits)))
-})
-
-test_that("countBreakpointOverlaps", {
-  expect_equal(countBreakpointOverlaps(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",
-    "chr1	100000	c	N	N[chr1:100200[	.	.	SVTYPE=BND;PARID=d",
-    "chr1	100200	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c"))),
-    breakpointRanges(.testrecord(c(
-      "chr1	200000	a	N	N[chr1:200100[	.	.	SVTYPE=BND;PARID=b",
-      "chr1	200100	b	N	]chr1:200000]N	.	.	SVTYPE=BND;PARID=a",
-      "chr1	100000	c	N	N[chr1:100200[	.	.	SVTYPE=BND;PARID=d",
-      "chr1	100200	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c")))),
-    c(0,0,1,1))
-})
-test_that("countBreakpointOverlaps uniqueAllocation", {
-  expect_equal(countBreakpointOverlaps(breakpointRanges(.testrecord(c(
-    "chr1	100000	a	N	N[chr1:100100[	1	.	SVTYPE=BND;PARID=b",
-    "chr1	100100	b	N	]chr1:100000]N	1	.	SVTYPE=BND;PARID=a",
-    "chr1	100000	c	N	N[chr1:100100[	2	.	SVTYPE=BND;PARID=d",
-    "chr1	100100	d	N	]chr1:100000]N	2	.	SVTYPE=BND;PARID=c"))),
-    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",
-      "chr1	100000	c	N	N[chr1:100100[	.	.	SVTYPE=BND;PARID=d",
-      "chr1	100100	d	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=c"))),
-    countOnlyBest=TRUE), c(0,0,2,2))
-})
-
-test_that("extractBreakpointSequence", {
-  expect_equal(extractBreakpointSequence(breakpointRanges(.testrecord(c(
-    # CTC>   <TGC
-    "chr1	100000	a	N	N[chr1:100100[	.	.	SVTYPE=BND;PARID=b",
-    "chr1	100100	b	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=a"
-  ))), hg19, anchoredBases=3), c("CTCTGC", "GCAGAG"))
-  expect_equal(extractBreakpointSequence(breakpointRanges(.testrecord(c(
-    # CTC> AC  <TGC
-    "chr1	100000	a	N	NAC[chr1:100100[	.	.	SVTYPE=BND;PARID=b",
-    "chr1	100100	b	N	]chr1:100000]ACN	.	.	SVTYPE=BND;PARID=a"
-  ))), hg19, anchoredBases=3), c("CTCACTGC", "GCAGTGAG"))
-  expect_equal(extractBreakpointSequence(breakpointRanges(.testrecord(c(
-    "chr12	1000000	a	N	[chr12:2000000[N	.	.	SVTYPE=BND;PARID=b", #GGATA
-    "chr12	2000000	b	N	[chr12:1000000[N	.	.	SVTYPE=BND;PARID=a"  #GAGAA
-  ))), hg19, anchoredBases=5), c("TATCCGAGAA", "TTCTCGGATA"))
-  expect_equal(extractBreakpointSequence(breakpointRanges(.testrecord(c(
-    "chr12	1000000	a	N	[chr12:2000000[N	.	.	SVTYPE=BND;PARID=b;CIPOS=-115,115",
-    "chr12	2000000	b	N	[chr12:1000000[N	.	.	SVTYPE=BND;PARID=a;CIPOS=-115,115"
-  ))), hg19, anchoredBases=5), c("TATCCGAGAA", "TTCTCGGATA"))
-  expect_equal(extractBreakpointSequence(breakpointRanges(.testrecord(c(
-    "chr1	9595627	a	A	A[chr1:9597590[	.	.	MATEID=b;SVTYPE=BND",
-    "chr1	9597590	b	C	]chr1:9595627]C	.	.	MATEID=a;SVTYPE=BND"
-  ))), hg19, anchoredBases=5)[1], "CTCCAAATCC")
-  expect_equal(extractBreakpointSequence(breakpointRanges(.testrecord(c(
-    "chr1	1	a	N	N[chr1:1[	.	.	MATEID=b;SVTYPE=BND",
-    "chr1	1	b	N	]chr1:1]N	.	.	MATEID=a;SVTYPE=BND"
-  ))), hg19, anchoredBases=2), c("NNNN", "NNNN"))
-  expect_equal(extractBreakpointSequence(breakpointRanges(.testrecord(c(
-    "chr1	1	a	N	N[chr1:1[	.	.	MATEID=b;SVTYPE=BND",
-    "chr1	1	b	N	]chr1:1]N	.	.	MATEID=a;SVTYPE=BND"
-  ))), hg19, 0, 0), c("", ""))
-  expect_equal(extractBreakpointSequence(breakpointRanges(.testrecord(c(
-    "chr1	1	a	N	N[chr1:1[	.	.	MATEID=b;SVTYPE=BND",
-    "chr1	1	b	N	]chr1:1]N	.	.	MATEID=a;SVTYPE=BND"
-  ))), hg19, 0, 1), c("N", "N"))
-})
-test_that("extractReferenceSequence", {
-  expect_equal(extractReferenceSequence(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"
-  ))), hg19, anchoredBases=3), c("CTCACT", "GCATGG"))
-  expect_equal(extractReferenceSequence(breakpointRanges(.testrecord(c(
-    "chr1	100000	a	N	NAC[chr1:100100[	.	.	SVTYPE=BND;PARID=b",
-    "chr1	100100	b	N	]chr1:100000]ACN	.	.	SVTYPE=BND;PARID=a"
-  ))), hg19, anchoredBases=3), c("CTCACT", "GCATGG"))
-  expect_equal(extractReferenceSequence(breakpointRanges(.testrecord(c(
-    "chr1	100000	a	N	NAC[chr1:100100[	.	.	SVTYPE=BND;PARID=b",
-    "chr1	100100	b	N	]chr1:100000]ACN	.	.	SVTYPE=BND;PARID=a"
-  ))), hg19, anchoredBases=3, followingBases=5), c("CTCACTAA", "GCATGGCG"))
-  expect_equal(extractReferenceSequence(breakpointRanges(.testrecord(c(
-    "chr1	100000	a	N	NAC[chr1:100100[	.	.	SVTYPE=BND;PARID=b;CIPOS=-5,5",
-    "chr1	100100	b	N	]chr1:100000]ACN	.	.	SVTYPE=BND;PARID=a;CIPOS=-5,5"
-  ))), hg19, anchoredBases=3, followingBases=5), c("CTCACTAA", "GCATGGCG"))
-  
-  expect_equal(extractReferenceSequence(breakpointRanges(.testrecord(c(
-    "chrM	1	a	G	]chrM:16571]G	.	.	SVTYPE=BND;PARID=b",
-    "chrM	16571	b	G	G[chrM:1[	.	.	SVTYPE=BND;PARID=a"
-  ))), hg19, anchoredBases=2, followingBases=3), c("TCNNN", "TGNNN"))
-})
-
-test_that("calculateReferenceHomology", {
-  expect_gte(calculateReferenceHomology(breakpointRanges(.testrecord(c(
-    "chr1	9595527	gridss43448o	A	A[chr1:9597585[	1502.22	.	CIPOS=-115,115;HOMLEN=230;HOMSEQ=TGGGAGGCTGAGGCAGGCAGATCACTTGAGGCCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTACTAAAAATACAGAAAAATTAGCCAGGCATGGTGGCACGTGCCTGTAATCCAGCTACTCGTGAGGCAGAGGCAGGAGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGTGACAGAG;MATEID=gridss43448h;SVTYPE=BND",
-    "chr1	9597585	gridss43448h	C	]chr1:9595527]C	1502.22	.	CIPOS=-115,115;HOMLEN=230;HOMSEQ=TGGGAGGCTGAGGCAGGCAGATCACTTGAGGCCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTACTAAAAATACAGAAAAATTAGCCAGGCATGGTGGCACGTGCCTGTAATCCAGCTACTCGTGAGGCAGAGGCAGGAGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCTGAGATCATGCCACTGCACTCCAGCCTGGGTGACAGAG;MATEID=gridss43448o;SVTYPE=BND"
-  ))), hg19)$inexacthomlen[1], 230)
-  
-  expect_lt(calculateReferenceHomology(breakpointRanges(.testrecord(c(
-    "chr12	1000000	a	A	A[chr12:2000000[	.	.	MATEID=b;SVTYPE=BND",
-    "chr12	2000000	b	C	]chr12:1000000]C	.	.	MATEID=a;SVTYPE=BND"
-  ))), hg19)$inexacthomlen[1], 3)
-  expect_equal(calculateReferenceHomology(breakpointRanges(.testrecord(c(
-    "chr1	1	a	A	A[chr1:1[	.	.	MATEID=b;SVTYPE=BND",
-    "chr1	1	b	C	]chr1:1]C	.	.	MATEID=a;SVTYPE=BND"
-  ))), hg19, 5)$inexacthomlen, c(NA,NA))
-  expect_true(is.na(calculateReferenceHomology(breakpointRanges(.testrecord(c(
-    "chr1	1	a	A	A[chr1:1[	.	.	MATEID=b;SVTYPE=BND",
-    "chr1	1	b	C	]chr1:1]C	.	.	MATEID=a;SVTYPE=BND",
-    "chr12	1000000	aa	A	A[chr12:2000000[	.	.	MATEID=bb;SVTYPE=BND",
-    "chr12	2000000	bb	C	]chr12:1000000]C	.	.	MATEID=aa;SVTYPE=BND"
-  ))), hg19, 5)$inexacthomlen[1]))
-})
-test_that("pairs_round_trip", {
-  for (f in c("gridss.bedpe", "unnamed.bedpe")) {
-    pairs = import(system.file("extdata", f, package = "StructuralVariantAnnotation"))
-    gr = pairs2breakpointgr(pairs)
-    pairs2 = breakpointgr2pairs(gr)
-    expect_equal(seqnames(S4Vectors::first(pairs)), seqnames(S4Vectors::first(pairs2)))
-    expect_equal(start(S4Vectors::first(pairs)), start(S4Vectors::first(pairs2)))
-    expect_equal(strand(S4Vectors::first(pairs)), strand(S4Vectors::first(pairs2)))
-    expect_equal(seqnames(S4Vectors::second(pairs)), seqnames(S4Vectors::second(pairs2)))
-    expect_equal(start(S4Vectors::second(pairs)), start(S4Vectors::second(pairs2)))
-    expect_equal(strand(S4Vectors::second(pairs)), strand(S4Vectors::second(pairs2)))
-    expect_equal(mcols(pairs)$name, mcols(pairs2)$name)
-    expect_equal(mcols(pairs)$score, mcols(pairs2)$score)
-  }
-})
-test_that("single_breakends_valididity", {
-  colo829_vcf = VariantAnnotation::readVcf(system.file("extdata", "COLO829T.purple.sv.ann.vcf.gz", package = "StructuralVariantAnnotation"))
-  colo829_bpgr <- breakpointRanges(colo829_vcf)
-  colo829_begr <- breakendRanges(colo829_vcf)
-  colo829_gr <- sort(c(colo829_begr, colo829_bpgr))
-  .assertValidBreakpointGRanges(colo829_gr, allowSingleBreakends=TRUE)
-  expect_error(.assertValidBreakpointGRanges(colo829_gr, allowSingleBreakends=FALSE))
-})
-
-#test_that("calculateBlastHomology", {
-#	Sys.setenv(PATH=paste(Sys.getenv("PATH"), "/usr/local/bioinf/bin", sep=":"))
-#	bh <- calculateBlastHomology(gr, hg19, "~/blastdb/16SMicrobial")
-#
-#})
-# test_that("performance_test_partner", {
-# 	n = 10000
-# 	gr = GRanges(
-# 		seqnames="1",
-# 		ranges=IRanges(start=1:(2*n), width=1),
-# 		partner=c(paste0(1:n, "o"), paste0(1:n, "h")))
-# 	names(gr)=c(paste0(1:n, "h"), paste0(1:n, "o"))
-# 	tictoc::tic(paste0("Start", n))
-# 	pgr = partner(gr)
-# 	tictoc::toc()
-# })
-test_that("simpleEventLength", {
-	expect_equal(simpleEventLength(breakpointRanges(.testrecord(c(
-			"chr1	100000	a	N	]chr1:100009]N	.	.	SVTYPE=BND;PARID=b",
-			"chr1	100009	b	N	N[chr1:100000[	.	.	SVTYPE=BND;PARID=a",
-			"chr1	100000	c	N	NNNNNNNNNNN[chr1:100001[	.	.	SVTYPE=BND;PARID=d",
-			"chr1	100001	d	N	]chr1:100000]NNNNNNNNNNN	.	.	SVTYPE=BND;PARID=c")))),
-		c(10, 10, 10, 10))
-	expect_equal(simpleEventLength(breakpointRanges(.testrecord(c(
-		"chr1	100000	a	N	N[chr1:100002[	.	.	SVTYPE=BND;PARID=b",
-		"chr1	100002	b	N	]chr1:100000]N	.	.	SVTYPE=BND;PARID=a")))),
-		c(-1, -1))
-})
-test_that("simpleEventType", {
-	expect_equal(simpleEventType(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"
-	)))), c("DEL", "DEL"))
-	expect_equal(simpleEventType(breakpointRanges(.testrecord(c(
-		"chr1	100000	a	N	]chr1:100100]N	.	.	SVTYPE=BND;PARID=b",
-		"chr1	100100	b	N	N[chr1:100000[	.	.	SVTYPE=BND;PARID=a"
-	)))), c("DUP", "DUP"))
-	expect_equal(simpleEventType(breakpointRanges(.testrecord(c(
-		"chr1	100000	a	N	NNNNNNNNNNNNNNNNNNNNNNNN[chr1:100001[	.	.	SVTYPE=BND;PARID=b",
-		"chr1	100001	b	N	]chr1:100000]NNNNNNNNNNNNNNNNNNNNNNNN	.	.	SVTYPE=BND;PARID=a"
-	)))), c("INS", "INS"))
-	expect_equal(simpleEventType(breakpointRanges(.testrecord(c(
-		"chr1	100000	a	N	NNNNNNNNNNNNNNNNNNNNNNNN[chr2:100001[	.	.	SVTYPE=BND;PARID=b",
-		"chr2	100001	b	N	]chr1:100000]NNNNNNNNNNNNNNNNNNNNNNNN	.	.	SVTYPE=BND;PARID=a"
-	)))), c("CTX", "CTX"))
-	expect_equal(simpleEventType(breakendRanges(.testrecord(c(
-		"chr1	100000	a	N	NNNNN.	.	.	SVTYPE=BND"
-	)))), c("BND"))
-})
-test_that("findInsDupOverlaps", {
-	gr1 = breakpointRanges(.testrecord(c(
-		"chr1	100000	a	N	]chr1:100009]N	.	.	SVTYPE=BND;PARID=b",
-		"chr1	100009	b	N	N[chr1:100000[	.	.	SVTYPE=BND;PARID=a",
-		"chr1	100000	c	N	NNNNNNNNNNN[chr1:100001[	.	.	SVTYPE=BND;PARID=d",
-		"chr1	100001	d	N	]chr1:100000]NNNNNNNNNNN	.	.	SVTYPE=BND;PARID=c")))
-	gr2 = 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",
-		"chr1	100000	c	N	NNNNNNNNNNN[chr1:100001[	.	.	SVTYPE=BND;PARID=d",
-		"chr1	100001	d	N	]chr1:100000]NNNNNNNNNNN	.	.	SVTYPE=BND;PARID=c")))
-	hits12 = findInsDupOverlaps(gr1, gr2, maxgap=1)
-	hits21 = findInsDupOverlaps(gr2, gr1, maxgap=1)
-	expect_equal(queryHits(hits12), c(1,2))
-	expect_equal(subjectHits(hits12), c(3,4))
-	# symmetrical
-	expect_equal(subjectHits(hits12), queryHits(hits21))
-	expect_equal(subjectHits(hits21), queryHits(hits12))
-})
-if (FALSE) {
-	transitiveGr = bpgr
-	subjectGr = bpgr
-	maximumInsertSize=700
-	maximumTransitiveBreakpoints=4
-	positionalMargin=8
-	impreciseTransitiveCalls=(transitiveGr$HOMLEN == 0 | is.null(transitiveGr$HOMLEN)) & start(transitiveGr) != end(transitiveGr)
-	impreciseSubjectCalls=(subjectGr$HOMLEN == 0 | is.null(subjectGr$HOMLEN)) & start(subjectGr) != end(subjectGr)
-	allowImprecise=FALSE
-}
-test_that("findTransitiveCalls imprecise", {
-	bpgr = breakpointRanges(.testrecord(c(
-		"chr1	100	bp1_1	N	N[chr2:200[	.	.	SVTYPE=BND;MATEID=bp1_2",
-		"chr2	200	bp1_2	N	]chr1:100]N	.	.	SVTYPE=BND;MATEID=bp1_1",
-		"chr2	300	bp2_1	N	N[chr3:500[	.	.	SVTYPE=BND;MATEID=bp2_2",
-		"chr3	500	bp2_2	N	]chr2:300]N	.	.	SVTYPE=BND;MATEID=bp2_1",
-		"chr1	50	imprecise_transitive_1	N	N[chr3:530[	.	.	SVTYPE=BND;MATEID=imprecise_transitive_2;IMPRECISE;CIPOS=-49,100",
-		"chr3	530	imprecise_transitive_2	N	]chr1:50]N	.	.	SVTYPE=BND;MATEID=imprecise_transitive_1;IMPRECISE;CIPOS=-100,100"
-	)))
-	transdf = findTransitiveCalls(bpgr, bpgr)
-	resultdf = DataFrame(
-			transitive_breakpoint_name=c("imprecise_transitive_1", "imprecise_transitive_2"),
-			total_distance=101,
-			traversed_breakpoint_names=CharacterList(c("bp1_1", "bp2_1"), c("bp2_2", "bp1_2")),
-			distance_to_traversed_breakpoint=IntegerList(c(0, 101), c(0, 101)))
-	expect_equal(transdf, resultdf)
-})
-test_that("findTransitiveCalls loop", {
-	bpgr = breakpointRanges(.testrecord(c(
-		"chr1	10000	bp1_1	N	N[chr2:100[	.	.	SVTYPE=BND;MATEID=bp1_2",
-		"chr2	100	bp1_2	N	]chr1:10000]N	.	.	SVTYPE=BND;MATEID=bp1_1",
-		"chr2	300	bp2_1	N	N[chr3:50000[	.	.	SVTYPE=BND;MATEID=bp2_2",
-		"chr3	50000	bp2_2	N	]chr2:300]N	.	.	SVTYPE=BND;MATEID=bp2_1",
-		"chr2	140	loop_1	N	]chr2:160]TTTTTN	.	.	SVTYPE=BND;MATEID=loop_2",
-		"chr2	160	loop_2	N	NTTTTT[chr2:140[	.	.	SVTYPE=BND;MATEID=loop_1",
-		"chr1	10050	imprecise_transitive_1	N	N[chr3:50030[	.	.	SVTYPE=BND;MATEID=imprecise_transitive_2;IMPRECISE;CIPOS=-60,60",
-		"chr3	50030	imprecise_transitive_2	N	]chr1:10050]N	.	.	SVTYPE=BND;MATEID=imprecise_transitive_1;IMPRECISE;CIPOS=-100,100"
-	)))
-	.us = function(df) as.data.frame(df) %>% mutate(
-		traversed_breakpoint_names=unstrsplit(traversed_breakpoint_names, ","),
-		distance_to_traversed_breakpoint=unstrsplit(CharacterList(distance_to_traversed_breakpoint), ","))
-	transdf = findTransitiveCalls(bpgr, bpgr, maximumTraversedBreakpoints=5) %>%
-		.us() %>%
-		dplyr::arrange(transitive_breakpoint_name, total_distance)
-	resultdf = DataFrame(
-		transitive_breakpoint_name=rep(c("imprecise_transitive_1", "imprecise_transitive_2"), each=4),
-		total_distance=rep(201 + 26*0:3, 2),
-		traversed_breakpoint_names=CharacterList(
-			c("bp1_1", "bp2_1"),
-			c("bp1_1", "loop_2", "bp2_1"),
-			c("bp1_1", "loop_2","loop_2", "bp2_1"),
-			c("bp1_1", "loop_2","loop_2","loop_2", "bp2_1"),
-			c("bp2_2", "bp1_2"),
-			c("bp2_2", "loop_1", "bp1_2"),
-			c("bp2_2", "loop_1", "loop_1", "bp1_2"),
-			c("bp2_2", "loop_1", "loop_1", "loop_1", "bp1_2")),
-		distance_to_traversed_breakpoint=IntegerList(
-			cumsum(c(0, 201)),
-			cumsum(c(0, 61+5, 161)),
-			cumsum(c(0, 61+5, 21+5, 161)),
-			cumsum(c(0, 61+5, 21+5, 21+5, 161)),
-			cumsum(c(0, 201)),
-			cumsum(c(0, 161+5, 61)),
-			cumsum(c(0, 161+5, 21+5, 61)),
-			cumsum(c(0, 161+5, 21+5, 21+5, 61)))) %>%
-		.us()
-	expect_equal(transdf, resultdf)
-})
-test_that(".traversable_segments", {
-	bpgr = breakpointRanges(.testrecord(c(
-		"chr1	10000	bp1_1	N	N[chr2:100[	.	.	SVTYPE=BND;MATEID=bp1_2",
-		"chr2	100	bp1_2	N	]chr1:10000]N	.	.	SVTYPE=BND;MATEID=bp1_1",
-		"chr2	300	bp2_1	N	N[chr3:50000[	.	.	SVTYPE=BND;MATEID=bp2_2",
-		"chr3	50000	bp2_2	N	]chr2:300]N	.	.	SVTYPE=BND;MATEID=bp2_1",
-		"chr2	140	loop_1	N	]chr2:160]TTTTTN	.	.	SVTYPE=BND;MATEID=loop_2",
-		"chr2	160	loop_2	N	NTTTTT[chr2:140[	.	.	SVTYPE=BND;MATEID=loop_1"
-	)))
-	#  -1 bp1    -loop-
-	#   |        |    |        +
-	#   2--------5----6--------3
-	#   -        -    +        |
-	#                          4-- bp2
-	#  100      140  160      300
-	# segments are:
-	#   2----------------------3
-	#   2-------------6
-	#            5-------------3
-	#
-	bpgr$ordinal = seq_len(length(bpgr))
-	bpgr$partnerOrdinal = partner(bpgr)$ordinal
-	segdf = .traversable_segments(bpgr, 1000)
-	expecteddf = data.frame(
-		segmentStartExternalOrdinal=c(1, 1, 6, 6),
-		segmentStartInternalOrdinal=c(2, 2, 5, 5),
-		segmentStartAdditionalLength=c(0,0,5,5),
-		segmentLength=c(61, 201, 161, 21),
-		segmentEndAdditionalLength=c(5, 0, 0, 5),
-		segmentEndInternalOrdinal=c(6, 3, 3, 6),
-		segmentEndExternalOrdinal=c(5, 4, 4, 5))
-	expecteddf = dplyr::bind_rows(expecteddf, expecteddf %>%
-		dplyr::select(
-			segmentStartExternalOrdinal=segmentEndExternalOrdinal,
-			segmentEndExternalOrdinal=segmentStartExternalOrdinal,
-			segmentLength=segmentLength,
-			segmentStartInternalOrdinal=segmentEndInternalOrdinal,
-			segmentEndInternalOrdinal=segmentStartInternalOrdinal,
-			segmentStartAdditionalLength=segmentEndAdditionalLength,
-			segmentEndAdditionalLength=segmentStartAdditionalLength))
-	expect_equal(
-		segdf %>% dplyr::arrange(segmentStartExternalOrdinal, segmentEndExternalOrdinal, segmentStartInternalOrdinal),
-		expecteddf %>% dplyr::arrange(segmentStartExternalOrdinal, segmentEndExternalOrdinal, segmentStartInternalOrdinal))
-})
-test_that("findTransitiveCalls precise", {
-	hundred_N="NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
-	two_hundred_N=paste0(hundred_N, hundred_N)
-	# chr1 --]100]
-	#          |
-	# chr2   [200[--------]300]
-	#                       |
-	# chr3                [100[----]220]
-	#                                |
-	# chr4                         [1000[-----
-	bpgr = breakpointRanges(.testrecord(c(
-		"chr1	100	bp1_1	N	N[chr2:200[	.	.	SVTYPE=BND;MATEID=bp1_2",
-		"chr2	200	bp1_2	N	]chr1:100]N	.	.	SVTYPE=BND;MATEID=bp1_1",
-		"chr2	300	bp2_1	N	N[chr3:100[	.	.	SVTYPE=BND;MATEID=bp2_2",
-		"chr3	100	bp2_2	N	]chr2:300]N	.	.	SVTYPE=BND;MATEID=bp2_1",
-		"chr3	220	bp3_1	N	N[chr4:1000[	.	.	SVTYPE=BND;MATEID=bp3_2",
-		"chr4	1000	bp3_2	N	]chr3:220]N	.	.	SVTYPE=BND;MATEID=bp3_1",
-		paste0("chr1	100	precise_transitive_1	N	N",two_hundred_N,"[chr4:1000[	.	.	SVTYPE=BND;MATEID=precise_transitive_2"),
-		paste0("chr4	1000	precise_transitive_2	N	]chr1:100]",two_hundred_N,"N	.	.	SVTYPE=BND;MATEID=precise_transitive_1")
-	)))
-	transdf = findTransitiveCalls(bpgr, bpgr)
-	resultdf = DataFrame(
-		transitive_breakpoint_name=c("precise_transitive_1", "precise_transitive_2"),
-		total_distance=101+121,
-		traversed_breakpoint_names=CharacterList(c("bp1_1", "bp2_1", "bp3_1"), c("bp3_2", "bp2_2", "bp1_2")),
-		distance_to_traversed_breakpoint=IntegerList(c(0, 101, 101+121), c(0, 121, 121+101)))
-	expect_equal(transdf, resultdf)
-})
-test_that("findTransitiveCalls long read colo829", {
-	t_vcf = list(
-		truth = readVcf(.testfile("truthset_somaticSVs_COLO829.vcf")),
-		nanosv = readVcf(.testfile("colo829_nanoSV_truth_overlap.vcf")))
-		#gridss = readVcf(.testfile("colo829_gridss_truth_overlap.vcf")))
-	t_bpgr = list()
-	for (n in names(t_vcf)) {
-		t_bpgr[[n]] = breakpointRanges(t_vcf[[n]], inferMissingBreakends=TRUE, ignoreUnknownSymbolicAlleles=TRUE)
-	}
-	t_bpgr$nanosv$insLen = pmax(0, info(t_vcf$nanosv[t_bpgr$nanosv$sourceId])$GAP)
-	transdf = findTransitiveCalls(t_bpgr$nanosv, t_bpgr$truth)
-	expect_equal(4, nrow(transdf))
-	#transitive_files = list(
-	#	truth = "C:/dev/colo829/truthset_somaticSVs_COLO829.vcf",
-	#	pbsv = "C:/dev/colo829/COLO829.somatic.pacbio.pbsv.vcf",
-	#	nanosv = "C:/dev/colo829/COLO829.nanopore.nanosv.vcf",
-	#	sniffles = "C:/dev/colo829/COLO829.nanopore.sniffles.vcf")
-	#gridss = "C:/dev/colo829/COLO829v001-colov1_gridss_COLO829v001T.gridss.unfiltered.vcf.gz")
-})