Variant caller based on cycle equivalence
Input GFA
Expect a sorted graph in GFA Expect first node to have id 1
Compile
cmake -H. -Bbuild && cmake --build build -- -j 3
Run
./bin/povu
Example
./bin/povu -v 2 call -i test_data/LPA.max120.gfa -- HG02572__LPA__tig00000001
Compile with debug symbols
cmake -DCMAKE_BUILD_TYPE=Debug -H. -Bbuild && cmake --build build -- -j 3
A release version (default)
cmake -DCMAKE_BUILD_TYPE=Release -H. -Bbuild && cmake --build build -- -j 3
You can use -t to generate the PVST in .pvst format which is a is a tab
separated plain text file made up of 5 columns as described below
| type | description |
|---|---|
| unsigned numeric | vertex id (can be zero) |
| list of unsigned numerics | child nodes in comma separated values |
| character | A value indicating whether the node is a true vertex or a dummy vertex (D for dummy, T for true) |
| unsigned numeric | the equivalence class of the vertex |
| unsigned numeric | the id of the vertex in the GFA file (multiple different vertex ids can share the same GFA id) |
0 T 6 1
1 T 6 2
2 0,1,3 D 6 1
3 10,14,15,4 D 6 2
4 5,9 T 4 3
5 6,7,8 T 2 4
6 T 1 5
7 T 3 6
8 T 2 7
9 T 4 8
10 11,12,13 T 7 9
11 T 0 10
12 T 8 11
13 T 7 12
14 T 6 13
15 T 6 14