SYNOPSIS

DESCRIPTION

-d|--debug

print detailed debugging messages to terminal (standard error)

-h|--help

print this help message and exit

-v|--version

print version number and exit

iLocus parsing:

-l|--delta: INT

when parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions; default is 500

-s|--skipends

when enumerating interval loci, exclude unannotated (and presumably incomplete) iLoci at either end of the sequence

-e|--endsonly

report only incomplete iLocus fragments at the unannotated ends of sequences (complement of --skipends)

-y|--skipiiloci

do not report intergenic iLoci

Refinement options:

-r|--refine

by default genes are grouped in the same iLocus if they have any overlap; 'refine' mode allows for a more nuanced handling of overlapping genes

-c|--cds

use CDS rather than UTRs for determining gene overlap; implies 'refine' mode

-m|--minoverlap: INT

the minimum number of nucleotides two genes must overlap to be grouped in the same iLocus; default is 1

Output options:

-n|--namefmt: STR

provide a printf-style format string to override the default ID format for newly created loci; default is 'locus%lu' (locus1, locus2, etc) for loci and 'iLocus%lu' (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value

-i|--ilens: FILE

create a file with the lengths of each intergenic iLocus

-g|--genemap: FILE

print a mapping from each gene annotation to its corresponding locus to the given file

-o|--outfile: FILE

name of file to which results will be written; default is terminal (standard output)

-T|--retainids

retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values

-t|--transmap: FILE

print a mapping from each transcript annotation to its corresponding locus to the given file

-V|--verbose

include all locus subfeatures (genes, RNAs, etc) in the GFF3 output; default includes only locus features

Input options:

-f|--filter: TYPE

comma-separated list of feature types to use in constructing loci/iLoci; default is 'gene'

-p|--parent: CT:PT

if a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature as a parent for any top-level mRNA feature; this option can be specified multiple times

-u|--pseudo

correct erroneously labeled pseudogenes