Each of the umi_tools
commands has a set of common options to deal
with input and output files, logging, profiling and debugging
By default, each tool reads from stdin
and outputs to stdout
,
with the exception of dedup
, group
and count
, which cannot
work from stdin
since in some cases they need to parse the input
multiple times.
By default, logging is sent to stdout
. In most cases, you will
want to direct this to a dedicated logfile (-L
/ --log
) or send
the logging to stderr
(--log2stderr
).
File to read stdin from [default = stdin].
File where output is to go [default = stdout].
File with logging information [default = stdout].
Send logging information to stderr [default = False].
Log level. The higher, the more output [default = 1].
File with error information [default = stderr].
Directory for temporary files. If not set, the bash environmental variable TMPDIR is used[default = None].
Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default (which is 9)
Store timeing information in file [default=none].
Name in timing file for this class of jobs [default=all].
Add header for timing information [default=none].
Random seed to initialize number generator with [default=none].