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