Initial commit

27 files changed, 247 insertions, 0 deletions

diff --git a/test-data/README.md b/test-data/README.md
new file mode 100644
index 0000000..fdee295
--- /dev/null
+++ b/test-data/README.md
@@ -0,0 +1,4 @@
+# Data source
+
+test1.gfa: https://github.com/pangenome/odgi/blob/5e58a324057ff094a11690968b9cf4b14ba14232/test/k.gfa
+test2.gfa: https://github.com/pangenome/odgi/blob/5e58a324057ff094a11690968b9cf4b14ba14232/test/note5.gfa
diff --git a/test-data/expected-output/test-crush.gfa b/test-data/expected-output/test-crush.gfa
new file mode 100644
index 0000000..9a86959
--- /dev/null
+++ b/test-data/expected-output/test-crush.gfa
@@ -0,0 +1,13 @@
+H	VN:Z:1.0
+S	1	ANA
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+L	1	+	3	-	0M
+S	2	A
+L	2	+	4	+	0M
+S	3	TC
+L	3	-	4	+	0M
+L	3	+	4	+	0M
+S	4	TNCAGGN
+P	5+	1+,3+,4+	*
+P	5-	1+,3-,4+	*
diff --git a/test-data/expected-output/test1-depth b/test-data/expected-output/test1-depth
new file mode 100644
index 0000000..3d5e7f5
--- /dev/null
+++ b/test-data/expected-output/test1-depth
@@ -0,0 +1,3 @@
+#path	start	end	mean.depth
+x	0	50	1.9
+y	0	50	1.9
diff --git a/test-data/expected-output/test1-depth-bed-windows b/test-data/expected-output/test1-depth-bed-windows
new file mode 100644
index 0000000..6ed8582
--- /dev/null
+++ b/test-data/expected-output/test1-depth-bed-windows
@@ -0,0 +1,11 @@
+#path	start	end	mean.depth
+x	0	10	1.8
+x	10	20	1.9
+x	20	30	2
+x	30	40	1.8
+x	40	50	2
+y	0	10	1.8
+y	10	20	1.9
+y	20	30	2
+y	30	40	1.8
+y	40	50	2
diff --git a/test-data/expected-output/test1-depth-graph-depth b/test-data/expected-output/test1-depth-graph-depth
new file mode 100644
index 0000000..04fd7d6
--- /dev/null
+++ b/test-data/expected-output/test1-depth-graph-depth
@@ -0,0 +1,16 @@
+#node.id	depth	depth.uniq
+1	2	2
+2	1	1
+3	1	1
+4	1	1
+5	1	1
+6	2	2
+7	1	1
+8	1	1
+9	2	2
+10	1	1
+11	1	1
+12	2	2
+13	1	1
+14	1	1
+15	2	2
diff --git a/test-data/expected-output/test1-matrix b/test-data/expected-output/test1-matrix
new file mode 100644
index 0000000..7839ceb
--- /dev/null
+++ b/test-data/expected-output/test1-matrix
@@ -0,0 +1,41 @@
+15 15 40
+1 2 1
+2 1 1
+1 3 1
+3 1 1
+2 4 1
+4 2 1
+2 5 1
+5 2 1
+3 4 1
+4 3 1
+3 5 1
+5 3 1
+4 6 1
+6 4 1
+5 6 1
+6 5 1
+6 7 1
+7 6 1
+6 8 1
+8 6 1
+7 9 1
+9 7 1
+8 9 1
+9 8 1
+9 10 1
+10 9 1
+9 11 1
+11 9 1
+10 12 1
+12 10 1
+11 12 1
+12 11 1
+12 13 1
+13 12 1
+12 14 1
+14 12 1
+13 15 1
+15 13 1
+14 15 1
+15 14 1
diff --git a/test-data/expected-output/test1-paths b/test-data/expected-output/test1-paths
new file mode 100644
index 0000000..b77b4eb
--- /dev/null
+++ b/test-data/expected-output/test1-paths
@@ -0,0 +1,2 @@
+x
+y
diff --git a/test-data/expected-output/test1-stats b/test-data/expected-output/test1-stats
new file mode 100644
index 0000000..a20d6a4
--- /dev/null
+++ b/test-data/expected-output/test1-stats
@@ -0,0 +1,2 @@
+#length	nodes	edges	paths	steps
+55	15	20	2	20
diff --git a/test-data/expected-output/test2-depth b/test-data/expected-output/test2-depth
new file mode 100644
index 0000000..d963e97
--- /dev/null
+++ b/test-data/expected-output/test2-depth
@@ -0,0 +1,3 @@
+#path	start	end	mean.depth
+5+	0	13	2
+5-	0	13	2
diff --git a/test-data/expected-output/test2-depth-bed-windows b/test-data/expected-output/test2-depth-bed-windows
new file mode 100644
index 0000000..45446de
--- /dev/null
+++ b/test-data/expected-output/test2-depth-bed-windows
@@ -0,0 +1,5 @@
+#path	start	end	mean.depth
+5+	0	10	2
+5+	10	13	2
+5-	0	10	2
+5-	10	13	2
diff --git a/test-data/expected-output/test2-depth-graph-depth b/test-data/expected-output/test2-depth-graph-depth
new file mode 100644
index 0000000..5769e3b
--- /dev/null
+++ b/test-data/expected-output/test2-depth-graph-depth
@@ -0,0 +1,5 @@
+#node.id	depth	depth.uniq
+1	2	2
+2	0	0
+3	2	2
+4	2	2
diff --git a/test-data/expected-output/test2-matrix b/test-data/expected-output/test2-matrix
new file mode 100644
index 0000000..3a4001b
--- /dev/null
+++ b/test-data/expected-output/test2-matrix
@@ -0,0 +1,13 @@
+4 4 12
+1 2 1
+2 1 1
+1 3 1
+3 1 1
+1 3 1
+3 1 1
+2 4 1
+4 2 1
+3 4 1
+4 3 1
+3 4 1
+4 3 1
diff --git a/test-data/expected-output/test2-paths b/test-data/expected-output/test2-paths
new file mode 100644
index 0000000..2bc98a9
--- /dev/null
+++ b/test-data/expected-output/test2-paths
@@ -0,0 +1,2 @@
+5+
+5-
diff --git a/test-data/expected-output/test2-stats b/test-data/expected-output/test2-stats
new file mode 100644
index 0000000..ec05936
--- /dev/null
+++ b/test-data/expected-output/test2-stats
@@ -0,0 +1,2 @@
+#length	nodes	edges	paths	steps
+14	4	6	2	6
diff --git a/test-data/expected-output/test3-depth b/test-data/expected-output/test3-depth
new file mode 100644
index 0000000..44daf00
--- /dev/null
+++ b/test-data/expected-output/test3-depth
@@ -0,0 +1,3 @@
+#path	start	end	mean.depth
+5+	0	20	2.7
+5-	0	13	2.53846
diff --git a/test-data/expected-output/test3-depth-bed-windows b/test-data/expected-output/test3-depth-bed-windows
new file mode 100644
index 0000000..b78d410
--- /dev/null
+++ b/test-data/expected-output/test3-depth-bed-windows
@@ -0,0 +1,5 @@
+#path	start	end	mean.depth
+5+	0	10	2.4
+5+	10	20	3
+5-	0	10	2.4
+5-	10	13	3
diff --git a/test-data/expected-output/test3-depth-graph-depth b/test-data/expected-output/test3-depth-graph-depth
new file mode 100644
index 0000000..1131a40
--- /dev/null
+++ b/test-data/expected-output/test3-depth-graph-depth
@@ -0,0 +1,5 @@
+#node.id	depth	depth.uniq
+1	2	2
+2	0	0
+3	2	2
+4	3	2
diff --git a/test-data/expected-output/test3-matrix b/test-data/expected-output/test3-matrix
new file mode 100644
index 0000000..3a4001b
--- /dev/null
+++ b/test-data/expected-output/test3-matrix
@@ -0,0 +1,13 @@
+4 4 12
+1 2 1
+2 1 1
+1 3 1
+3 1 1
+1 3 1
+3 1 1
+2 4 1
+4 2 1
+3 4 1
+4 3 1
+3 4 1
+4 3 1
diff --git a/test-data/expected-output/test3-paths b/test-data/expected-output/test3-paths
new file mode 100644
index 0000000..2bc98a9
--- /dev/null
+++ b/test-data/expected-output/test3-paths
@@ -0,0 +1,2 @@
+5+
+5-
diff --git a/test-data/expected-output/test3-stats b/test-data/expected-output/test3-stats
new file mode 100644
index 0000000..9f48a71
--- /dev/null
+++ b/test-data/expected-output/test3-stats
@@ -0,0 +1,2 @@
+#length	nodes	edges	paths	steps
+14	4	6	2	7
diff --git a/test-data/test-crush.gfa b/test-data/test-crush.gfa
new file mode 100644
index 0000000..e9c601b
--- /dev/null
+++ b/test-data/test-crush.gfa
@@ -0,0 +1,13 @@
+H	VN:Z:1.0
+S	1	ANNA
+S	2	A
+S	3	TC
+S	4	TNNCAGGNNNN
+P	5+	1+,3+,4+
+P	5-	1+,3-,4+
+L	1	+	2	+
+L	1	+	3	+
+L	1	+	3	-
+L	3	-	4	+
+L	2	+	4	+
+L	3	+	4	+
diff --git a/test-data/test1-bed-windows b/test-data/test1-bed-windows
new file mode 100644
index 0000000..48f9f6c
--- /dev/null
+++ b/test-data/test1-bed-windows
@@ -0,0 +1,10 @@
+x	0	10
+x	10	20
+x	20	30
+x	30	40
+x	40	50
+y	0	10
+y	10	20
+y	20	30
+y	30	40
+y	40	50
diff --git a/test-data/test1.gfa b/test-data/test1.gfa
new file mode 100644
index 0000000..b11f390
--- /dev/null
+++ b/test-data/test1.gfa
@@ -0,0 +1,38 @@
+H	VN:Z:1.0
+S	1	CAAATAAG
+S	2	A
+S	3	G
+S	4	T
+S	5	C
+S	6	TTG
+S	7	A
+S	8	G
+S	9	AAATTTTCTGGAGTTCTAT
+S	10	A
+S	11	T
+S	12	ATAT
+S	13	A
+S	14	T
+S	15	CCAACTCTCTG
+P	x	1+,3+,5+,6+,8+,9+,11+,12+,14+,15+	8M,1M,1M,3M,1M,19M,1M,4M,1M,11M
+P	y	1+,2+,4+,6+,7+,9+,10+,12+,13+,15+	8M,1M,1M,3M,1M,19M,1M,4M,1M,11M
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+L	2	+	4	+	0M
+L	2	+	5	+	0M
+L	3	+	4	+	0M
+L	3	+	5	+	0M
+L	4	+	6	+	0M
+L	5	+	6	+	0M
+L	6	+	7	+	0M
+L	6	+	8	+	0M
+L	7	+	9	+	0M
+L	8	+	9	+	0M
+L	9	+	10	+	0M
+L	9	+	11	+	0M
+L	10	+	12	+	0M
+L	11	+	12	+	0M
+L	12	+	13	+	0M
+L	12	+	14	+	0M
+L	13	+	15	+	0M
+L	14	+	15	+	0M
diff --git a/test-data/test2-bed-windows b/test-data/test2-bed-windows
new file mode 100644
index 0000000..8242604
--- /dev/null
+++ b/test-data/test2-bed-windows
@@ -0,0 +1,4 @@
+5+	0	10
+5+	10	13
+5-	0	10
+5-	10	13
diff --git a/test-data/test2.gfa b/test-data/test2.gfa
new file mode 100644
index 0000000..f305609
--- /dev/null
+++ b/test-data/test2.gfa
@@ -0,0 +1,13 @@
+H	VN:Z:1.0
+S	1	AGGA
+S	2	A
+S	3	TC
+S	4	TCTCAGG
+P	5+	1+,3+,4+	8M,1M,1M
+P	5-	1+,3-,4+	8M,1M,1M
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+L	1	+	3	-	0M
+L	3	-	4	+	0M
+L	2	+	4	+	0M
+L	3	+	4	+	0M
diff --git a/test-data/test3-bed-windows b/test-data/test3-bed-windows
new file mode 100644
index 0000000..23cc623
--- /dev/null
+++ b/test-data/test3-bed-windows
@@ -0,0 +1,4 @@
+5+	0	10
+5+	10	20
+5-	0	10
+5-	10	13
diff --git a/test-data/test3.gfa b/test-data/test3.gfa
new file mode 100644
index 0000000..1a28506
--- /dev/null
+++ b/test-data/test3.gfa
@@ -0,0 +1,13 @@
+H	VN:Z:1.0
+S	1	AGGA
+S	2	A
+S	3	TC
+S	4	TCTCAGG
+P	5+	1+,3+,4+,4+	8M,1M,1M
+P	5-	1+,3-,4+	8M,1M,1M
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+L	1	+	3	-	0M
+L	3	-	4	+	0M
+L	2	+	4	+	0M
+L	3	+	4	+	0M