######### odgi untangle #########
Project paths into reference-relative BEDPE, to decompose paralogy relationships.
odgi untangle [-i, --input=FILE] [OPTION]…
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.
MANDATORY OPTIONS --------------
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 ----------------
Use this query path.
Use this target (reference) path.
Use query paths listed in FILE. Each line must contain one path.
Use target (reference) paths list (one per line) in FILE.
Merge segments shorter than this length into previous segments.
Report up to the Nth best target (reference) mapping for each query segment (default: 1).
Report target mappings >= the given jaccard threshold, with 0 <= N <= 1.0 (default: 0.0).
Cut every N base pairs of the sorted graph (default: 0/OFF).
Emit the output in PAF format.
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.
Emit node identifiers where segment boundaries started (one identifier per row).
Render a table showing the positional dotplot of the query against itself.
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).
Number of threads to use for parallel operations.
Print information about the operations and the progress to stderr.
Print a help message for odgi untangle.