From 586428723f40d929f3ef9402352378c6d6629841 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 28 Aug 2026 03:05:32 +0100 Subject: Bridge extracted subpaths. --- .../expected-output/test-extract-path-bridge-0.gfa | 9 +++++ .../expected-output/test-extract-path-bridge-1.gfa | 9 +++++ .../expected-output/test-extract-path-bridge-2.gfa | 9 +++++ .../expected-output/test-extract-path-bridge-3.gfa | 13 ++++++ .../expected-output/test1-extract-bed-windows.gfa | 46 ++++++++++++++++++++++ .../test1-extract-path-no-bridge-10-20.gfa | 9 ----- .../expected-output/test2-extract-bed-windows.gfa | 12 ++++++ .../expected-output/test3-extract-bed-windows.gfa | 13 ++++++ 8 files changed, 111 insertions(+), 9 deletions(-) create mode 100644 test-data/expected-output/test-extract-path-bridge-0.gfa create mode 100644 test-data/expected-output/test-extract-path-bridge-1.gfa create mode 100644 test-data/expected-output/test-extract-path-bridge-2.gfa create mode 100644 test-data/expected-output/test-extract-path-bridge-3.gfa create mode 100644 test-data/expected-output/test1-extract-bed-windows.gfa delete mode 100644 test-data/expected-output/test1-extract-path-no-bridge-10-20.gfa create mode 100644 test-data/expected-output/test2-extract-bed-windows.gfa create mode 100644 test-data/expected-output/test3-extract-bed-windows.gfa (limited to 'test-data/expected-output') diff --git a/test-data/expected-output/test-extract-path-bridge-0.gfa b/test-data/expected-output/test-extract-path-bridge-0.gfa new file mode 100644 index 0000000..96dae01 --- /dev/null +++ b/test-data/expected-output/test-extract-path-bridge-0.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-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/test1-extract-path-no-bridge-10-20.gfa b/test-data/expected-output/test1-extract-path-no-bridge-10-20.gfa deleted file mode 100644 index 4846f99..0000000 --- a/test-data/expected-output/test1-extract-path-no-bridge-10-20.gfa +++ /dev/null @@ -1,9 +0,0 @@ -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:14-33 9+ * 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+ * -- cgit 1.4.1