odgi break¶
break cycles in the graph and drop its paths
SYNOPSIS¶
odgi break [-i, –idx=FILE] [-o, –out=FILE] [OPTION]…
DESCRIPTION¶
The odgi break(1) command finds cycles in a graph via breadth-first search (BFS) and breaks them, also dropping the graph’s paths.
OPTIONS¶
Graph Files IO¶
-i, –idx=FILE
File containing the succinct variation graph to break. The file name
usually ends with .og.
-o, –out=FILE
Write the broken graph to FILE.
Cycle Options¶
-c, –cycle-max-bp=N
The maximum cycle length at which to break.
-s, –max-search-bp=N
The maximum search space of each BFS given in number of base pairs.
-u, –repeat-up-to=N
Iterate cycle breaking up to N times or stop if no new edges are
removed.
-d, –show
Print the edges we would remove to stdout.
Program Information¶
-h, –help
Print a help message for odgi break.