######### odgi paths #########
Interrogate the embedded paths of a graph. Does not print anything to stdout by default!
odgi paths [-i, --idx=FILE] [OPTION]…
The odgi paths command allows the investigation of paths of a given variation graph. It can calculate overlap statistics of groupings of paths.
MANDATORY OPTIONS --------------
-i, --idx=FILE
Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!
Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!
Path Investigation Options ---------------------
-O, --overlaps=FILE
Read in the path grouping FILE to generate the overlap statistics from. The file must be tab-delimited. The first column lists a grouping and the second the path itself. Each line has one path entry. For each group the pairwise overlap statistics for each pairing will be calculated and printed to stdout.
Read in the path grouping FILE to generate the overlap statistics from. The file must be tab-delimited. The first column lists a grouping and the second the path itself. Each line has one path entry. For each group the pairwise overlap statistics for each pairing will be calculated and printed to stdout.
-L, --list-paths
Print the paths in the graph to stdout. Each path is printed in its own line.
Print the paths in the graph to stdout. Each path is printed in its own line.
-l, --list-paths-start-end
If -L,--list-paths was specified, this additionally prints the start and end positions of each path in additional, tab-delimited coloumns.
If -L,--list-paths was specified, this additionally prints the start and end positions of each path in additional, tab-delimited coloumns.
-f, --fasta
Print paths in FASTA format to stdout. One line for the FASTA header, another line for the whole sequence.
Print paths in FASTA format to stdout. One line for the FASTA header, another line for the whole sequence.
-H, --haplotypes
Print to stdout the paths in an approximate binary haplotype matrix based on the graph’s sort order. The output is tab-delimited: path.name, path.length, path.step.count, node.1, node.2, node.n. Each path entry is printed in its own line.
Print to stdout the paths in an approximate binary haplotype matrix based on the graph’s sort order. The output is tab-delimited: path.name, path.length, path.step.count, node.1, node.2, node.n. Each path entry is printed in its own line.
-N, --scale-by-node-len
Scale the haplotype matrix cells by node length.
Scale the haplotype matrix cells by node length.
-D, --delim=CHAR
The part of each path name before this delimiter is a group identifier. For use with -H, --haplotypes: it prints an additional, first column group.name to stdout.
The part of each path name before this delimiter is a group identifier. For use with -H, --haplotypes: it prints an additional, first column group.name to stdout.
-p, --delim-pos=N
Consider the N-th occurrence of the delimiter specified with -D, --delim to obtain the group identifier. Specify 1 for the 1st occurrence (default)."
Consider the N-th occurrence of the delimiter specified with -D, --delim to obtain the group identifier. Specify 1 for the 1st occurrence (default)."
Path Modification Options ---------------------| -K, --keep-paths=[FILE] | Keep paths listed (by line) in FILE.
-X, --drop-paths=[FILE]
Drop paths listed (by line) in FILE.
Drop paths listed (by line) in FILE.
-o, --out=FILE
Write the dynamic succinct variation graph to this file (e.g. .og)
Write the dynamic succinct variation graph to this file (e.g. .og)
-t, --threads=N
Number of threads to use for parallel operations.
Number of threads to use for parallel operations.
-P, --progress
Print information about the operations and the progress to stderr.
Print information about the operations and the progress to stderr.
-h, --help
Print a help message for odgi paths.
Print a help message for odgi paths.