Bridge extracted subpaths. HEAD main

8 files changed, 121 insertions, 1 deletions

diff --git a/test-data/expected-output/test1-extract-path-no-bridge-10-20.gfa b/test-data/expected-output/test-extract-path-bridge-0.gfa
index 4846f99..96dae01 100644
--- a/test-data/expected-output/test1-extract-path-no-bridge-10-20.gfa
+++ b/test-data/expected-output/test-extract-path-bridge-0.gfa
@@ -6,4 +6,4 @@ L	8	+	9	+	0M
 S	9	AAATTTTCTGGAGTTCTAT
 P	x:10-33	6+,8+,9+	*
 P	y:10-13	6+	*
-P	y:14-33	9+	*
+P	y:16-35	9+	*
diff --git a/test-data/expected-output/test-extract-path-bridge-1.gfa b/test-data/expected-output/test-extract-path-bridge-1.gfa
new file mode 100644
index 0000000..96dae01
--- /dev/null
+++ b/test-data/expected-output/test-extract-path-bridge-1.gfa
@@ -0,0 +1,9 @@
+H	VN:Z:1.0
+S	6	TTG
+L	6	+	8	+	0M
+S	8	G
+L	8	+	9	+	0M
+S	9	AAATTTTCTGGAGTTCTAT
+P	x:10-33	6+,8+,9+	*
+P	y:10-13	6+	*
+P	y:16-35	9+	*
diff --git a/test-data/expected-output/test-extract-path-bridge-2.gfa b/test-data/expected-output/test-extract-path-bridge-2.gfa
new file mode 100644
index 0000000..96dae01
--- /dev/null
+++ b/test-data/expected-output/test-extract-path-bridge-2.gfa
@@ -0,0 +1,9 @@
+H	VN:Z:1.0
+S	6	TTG
+L	6	+	8	+	0M
+S	8	G
+L	8	+	9	+	0M
+S	9	AAATTTTCTGGAGTTCTAT
+P	x:10-33	6+,8+,9+	*
+P	y:10-13	6+	*
+P	y:16-35	9+	*
diff --git a/test-data/expected-output/test-extract-path-bridge-3.gfa b/test-data/expected-output/test-extract-path-bridge-3.gfa
new file mode 100644
index 0000000..7ccf7e8
--- /dev/null
+++ b/test-data/expected-output/test-extract-path-bridge-3.gfa
@@ -0,0 +1,13 @@
+H	VN:Z:1.0
+S	6	TTG
+L	6	+	7	+	0M
+L	6	+	8	+	0M
+S	7	AG
+L	7	+	10	+	0M
+S	8	G
+L	8	+	9	+	0M
+S	9	AAATTTTCTGGAGTTCTAT
+S	10	A
+L	10	+	9	+	0M
+P	x:10-33	6+,8+,9+	*
+P	y:10-35	6+,7+,10+,9+	*
diff --git a/test-data/expected-output/test1-extract-bed-windows.gfa b/test-data/expected-output/test1-extract-bed-windows.gfa
new file mode 100644
index 0000000..ba2bd79
--- /dev/null
+++ b/test-data/expected-output/test1-extract-bed-windows.gfa
@@ -0,0 +1,46 @@
+H	VN:Z:1.0
+S	1	CAAATAAG
+L	1	+	2	+	0M
+L	1	+	3	+	0M
+S	2	A
+L	2	+	4	+	0M
+L	2	+	5	+	0M
+S	3	G
+L	3	+	4	+	0M
+L	3	+	5	+	0M
+S	4	T
+L	4	+	6	+	0M
+S	5	C
+L	5	+	6	+	0M
+S	6	TTG
+L	6	+	7	+	0M
+L	6	+	8	+	0M
+S	7	A
+L	7	+	9	+	0M
+S	8	G
+L	8	+	9	+	0M
+S	9	AAATTTTCTGGAGTTCTAT
+L	9	+	10	+	0M
+L	9	+	11	+	0M
+S	10	A
+L	10	+	12	+	0M
+S	11	T
+L	11	+	12	+	0M
+S	12	ATAT
+L	12	+	13	+	0M
+L	12	+	14	+	0M
+S	13	A
+L	13	+	15	+	0M
+S	14	T
+L	14	+	15	+	0M
+S	15	CCAACTCTCTG
+P	x:0-10	1+,3+,5+	*
+P	x:10-33	6+,8+,9+	*
+P	x:14-33	9+	*
+P	x:14-50	9+,11+,12+,14+,15+	*
+P	x:39-50	15+	*
+P	y:0-10	1+,2+,4+	*
+P	y:10-33	6+,7+,9+	*
+P	y:14-33	9+	*
+P	y:14-50	9+,10+,12+,13+,15+	*
+P	y:39-50	15+	*
diff --git a/test-data/expected-output/test2-extract-bed-windows.gfa b/test-data/expected-output/test2-extract-bed-windows.gfa
new file mode 100644
index 0000000..bd0b466
--- /dev/null
+++ b/test-data/expected-output/test2-extract-bed-windows.gfa
@@ -0,0 +1,12 @@
+H	VN:Z:1.0
+S	1	AGGA
+L	1	+	3	+	0M
+L	1	+	3	-	0M
+S	3	TC
+L	3	+	4	+	0M
+S	4	TCTCAGG
+L	4	-	3	+	0M
+P	5+:0-13	1+,3+,4+	*
+P	5+:6-13	4+	*
+P	5-:0-13	1+,3-,4+	*
+P	5-:6-13	4+	*
diff --git a/test-data/expected-output/test3-extract-bed-windows.gfa b/test-data/expected-output/test3-extract-bed-windows.gfa
new file mode 100644
index 0000000..8fbb0bc
--- /dev/null
+++ b/test-data/expected-output/test3-extract-bed-windows.gfa
@@ -0,0 +1,13 @@
+H	VN:Z:1.0
+S	1	AGGA
+L	1	+	3	+	0M
+L	1	+	3	-	0M
+S	3	TC
+L	3	+	4	+	0M
+S	4	TCTCAGG
+L	4	-	3	+	0M
+L	4	+	4	+	0M
+P	5+:0-13	1+,3+,4+	*
+P	5+:6-20	4+,4+	*
+P	5-:0-13	1+,3-,4+	*
+P	5-:6-13	4+	*
diff --git a/test-data/test-extract-path-bridge.gfa b/test-data/test-extract-path-bridge.gfa
new file mode 100644
index 0000000..1f2846f
--- /dev/null
+++ b/test-data/test-extract-path-bridge.gfa
@@ -0,0 +1,18 @@
+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	AG
+S	8	G
+S	9	AAATTTTCTGGAGTTCTAT
+S	10	A
+L	6	+	7	+
+L	6	+	8	+
+L	7	+	10	+
+L	8	+	9	+
+L	10	+	9	+
+P	x	1+,3+,5+,6+,8+,9+
+P	y	1+,2+,4+,6+,7+,10+,9+