Options

usage: trcls [-h] [--map-tolerance MAP_TOLERANCE]
             [--skip-tolerance SKIP_TOLERANCE]
             [--junction-tolerance JUNCTION_TOLERANCE] [--quiet] [--verbose]
             [--very-verbose] [--version]
             [alignment] [features]

Positional Arguments

alignment

a SAM alignment file

features

a GTF annotation file

Named Arguments

--map-tolerance, -m

number of nt which must map to reference in sequence to be considered a feature, e.g. exon (default: 10)

Default: 10

--skip-tolerance, -s

number of non-splice reference skips allowed, e.g. in deletions (default: 20)

Default: 20

--junction-tolerance, -o

number of nt exon-intron junctions allowed to mismatch by (default: 20)

Default: 20

--quiet, -q

show only error (ERROR) messages

Default: False

--verbose, -v

show verbose (INFO, WARNING, ERROR) messages

Default: False

--very-verbose, -vv

show very verbose (DEBUG, INFO, WARNING, ERROR) messages

Default: False

--version

Print the version number

Default: False