diff options
Diffstat (limited to 'test-data')
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 |