From d2282f6b7453a023af92424309e8713f5c8f7ca7 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Tue, 18 Aug 2026 14:44:46 +0100
Subject: Add chop subcommand.

---
 test-data/expected-output/test3-chop-1.gfa | 33 ++++++++++++++++++++++++++++++
 test-data/expected-output/test3-chop-2.gfa | 21 +++++++++++++++++++
 test-data/expected-output/test3-chop-3.gfa | 19 +++++++++++++++++
 test-data/expected-output/test3-chop-4.gfa | 15 ++++++++++++++
 4 files changed, 88 insertions(+)
 create mode 100644 test-data/expected-output/test3-chop-1.gfa
 create mode 100644 test-data/expected-output/test3-chop-2.gfa
 create mode 100644 test-data/expected-output/test3-chop-3.gfa
 create mode 100644 test-data/expected-output/test3-chop-4.gfa

(limited to 'test-data/expected-output')

diff --git a/test-data/expected-output/test3-chop-1.gfa b/test-data/expected-output/test3-chop-1.gfa
new file mode 100644
index 0000000..fa89dce
--- /dev/null
+++ b/test-data/expected-output/test3-chop-1.gfa
@@ -0,0 +1,33 @@
+H	VN:Z:1.0
+S	1	A
+L	1	+	2	+	0M
+S	2	G
+L	2	+	3	+	0M
+S	3	G
+L	3	+	4	+	0M
+S	4	A
+L	4	+	5	+	0M
+L	4	+	6	+	0M
+S	5	A
+L	5	+	8	+	0M
+S	6	T
+L	6	+	7	+	0M
+L	6	-	8	+	0M
+S	7	C
+L	7	+	4	-	0M
+L	7	+	8	+	0M
+S	8	T
+L	8	+	9	+	0M
+S	9	C
+L	9	+	10	+	0M
+S	10	T
+L	10	+	11	+	0M
+S	11	C
+L	11	+	12	+	0M
+S	12	A
+L	12	+	13	+	0M
+S	13	G
+L	13	+	14	+	0M
+S	14	G
+P	5+	1+,2+,3+,4+,6+,7+,8+,9+,10+,11+,12+,13+,14+,8+,9+,10+,11+,12+,13+,14+	*
+P	5-	1+,2+,3+,4+,7-,6-,8+,9+,10+,11+,12+,13+,14+	*
diff --git a/test-data/expected-output/test3-chop-2.gfa b/test-data/expected-output/test3-chop-2.gfa
new file mode 100644
index 0000000..bdc77d3
--- /dev/null
+++ b/test-data/expected-output/test3-chop-2.gfa
@@ -0,0 +1,21 @@
+H	VN:Z:1.0
+S	1	AG
+L	1	+	2	+	0M
+S	2	GA
+L	2	+	3	+	0M
+L	2	+	4	+	0M
+L	2	+	4	-	0M
+S	3	A
+L	3	+	5	+	0M
+S	4	TC
+L	4	-	5	+	0M
+L	4	+	5	+	0M
+S	5	TC
+L	5	+	6	+	0M
+S	6	TC
+L	6	+	7	+	0M
+S	7	AG
+L	7	+	8	+	0M
+S	8	G
+P	5+	1+,2+,4+,5+,6+,7+,8+,5+,6+,7+,8+	*
+P	5-	1+,2+,4-,5+,6+,7+,8+	*
diff --git a/test-data/expected-output/test3-chop-3.gfa b/test-data/expected-output/test3-chop-3.gfa
new file mode 100644
index 0000000..0e16301
--- /dev/null
+++ b/test-data/expected-output/test3-chop-3.gfa
@@ -0,0 +1,19 @@
+H	VN:Z:1.0
+S	1	AGG
+L	1	+	2	+	0M
+S	2	A
+L	2	+	3	+	0M
+L	2	+	4	+	0M
+L	2	+	4	-	0M
+S	3	A
+L	3	+	5	+	0M
+S	4	TC
+L	4	-	5	+	0M
+L	4	+	5	+	0M
+S	5	TCT
+L	5	+	6	+	0M
+S	6	CAG
+L	6	+	7	+	0M
+S	7	G
+P	5+	1+,2+,4+,5+,6+,7+,5+,6+,7+	*
+P	5-	1+,2+,4-,5+,6+,7+	*
diff --git a/test-data/expected-output/test3-chop-4.gfa b/test-data/expected-output/test3-chop-4.gfa
new file mode 100644
index 0000000..f043b82
--- /dev/null
+++ b/test-data/expected-output/test3-chop-4.gfa
@@ -0,0 +1,15 @@
+H	VN:Z:1.0
+S	1	AGGA
+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	TCTC
+L	4	+	5	+	0M
+S	5	AGG
+P	5+	1+,3+,4+,5+,4+,5+	*
+P	5-	1+,3-,4+,5+	*
-- 
cgit 1.4.1