odgi untangle
Project paths into reference-relative BEDPE, to decompose paralogy relationships.
SYNOPSIS
odgi untangle [-i, --input=FILE] [OPTION]…
DESCRIPTION
The odgi untangle command projects paths into a reference-relative BEDPE file, decomposing paralogy relationships. During this process, it is capable of untangling loopy region resulting in linearized pairs of regions in the BEDPE file. A self dotplot assists in debugging and understanding the untangle process.
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!
Untangling Options
-q, --query-path=NAME
Use this query path.
-r, --target-path=NAME
Use this target (reference) path.
-Q, --query-paths=FILE
Use query paths listed in FILE. Each line must contain one path.
-R, --target-paths=FILE
Use target (reference) paths list (one per line) in FILE.
-m, --merge-dist=N
Merge segments shorter than this length into previous segments.
-n, --n-best=N
Report up to the N*th best target (reference) mapping for each query segment (default: *1).
-j, --min-jaccard=N
Report target mappings >= the given jaccard threshold, with 0 <= N <= 1.0 (default: 0.0).
-e, --cut-every=N
Cut every N base pairs of the sorted graph (default: 0/OFF).
-p, --paf-output
Emit the output in PAF format.
-c, --cut-points-input=FILE
A text file of node identifiers (one identifier per row) where to start the segment boundaries. When specified, no further starting points will be added.
-d, --cut-points-output=FILE
Emit node identifiers where segment boundaries started (one identifier per row).
Debugging Options
-s, --self-dotplot
Render a table showing the positional dotplot of the query against itself.
Step Index Options
-a, --step-index=FILE
Load the step index from this FILE. The file name usually ends with .stpidx. (default: build the step index from scratch with a sampling rate of 8).
Threading
-t, --threads=N
Number of threads to use for 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 untangle.