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povu

Variant caller based on cycle equivalence

Input

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

Development

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

Pangenome Variation Structure Tree (PVST)

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)

Example

graph pvst

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

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