odgi depth

Find the depth of a graph as defined by query criteria. Depth can be node-depth computed by counting all defined paths that run through a node. By default it prints in a tab-delimited format path, start, end, and mean.depth to stdout.

SYNOPSIS

odgi depth [-i, --input=FILE] [OPTION]…

DESCRIPTION

The odgi depth command finds the depth of graph as defined by query criteria. Without specifying any non-mandatory options, it prints in a tab-delimited format path, start, end, and mean.depth to stdout.

OPTIONS

MANDATORY OPTIONS

-i, --input=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!

Depth Options

-s, --subset-paths=FILE

Compute the depth considering only paths specified in FILE. The file must contain one path name per line and a subset of all paths can be specified. If a step is of a path of the given list, it is taken into account when calculating a node's depth.

-r, --path=STRING

Compute the depth of the given path STRING in the graph.

-R, --paths=FILE

Report the depth only for the paths listed in FILE.

-g, --graph-pos=[[node_id][,offset[,(+|-)]**]**]

Compute the depth at the given node e.g. 7 or 3,4 or 42,10,+ or 302,0,-.

-G, --graph-pos-file=FILE

A file with one graph path position per line.

-p, --path-pos=[[path_name][,offset[,(+|-)]**]**]

Return depth at the given path position e.g. chrQ or chr3,42 or chr8,1337,+ or chrZ,3929,-.

-F, --path-pos-file=FILE

A file with one path position per line.

-b, --bed-input=FILE

A BED file of ranges in paths in the graph.

-d, --graph-depth-table

Compute the depth and unique depth on each node in the graph, writing a table by node:

node.id, depth, and depth.uniq.

-v, --graph-depth-vec

Compute the depth on each node in the graph, writing a vector by base in one line.

-D, --path-depth

Compute a vector of depth on each base of each path. Each line consists of a path name and subsequently the space-separated depth of each base.

-a, --self-depth

Compute the depth of the path versus itself on each base in each path. Each line consists of a path name and subsequently the space-separated depth of each base.

-S, --summarize

Provide a summary of the depth distribution in the graph. In a tab-delimited format it prints to stdout: node.count, graph.length, step.count, path.length, mean.node.depth (step.count/node.count), and mean.graph.depth (path.length/graph.length).

-w, --windows-in=LEN:MIN:MAX

Print to stdout a BED file of path intervals where the depth is between MIN and MAX, merging the ranges not separated by more then LEN bp.

-W, --windows-out=LEN:MIN:MAX

Print to stdout a BED file of path intervals where the depth is outside MIN and MAX, merging the ranges not separated by more then LEN bp.

Threading

-t, --threads=N

Number of threads to use in parallel operations.

Processing Information

-P, --progress

Print information about the operations and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi depth.