Common options¶
Each of the umi_tools commands has a set of common options to deal
with input and output files, logging, profiling and debugging
Input/Output options¶
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).
-I, --stdin¶
File to read stdin from [default = stdin].
-S, --stdout¶
File where output is to go [default = stdout].
-L, --log¶
File with logging information [default = stdout].
--log2stderr¶
Send logging information to stderr [default = False].
-v, --verbose¶
Log level. The higher, the more output [default = 1].
-E, --error¶
File with error information [default = stderr].
--temp-dir¶
Directory for temporary files. If not set, the bash environmental variable TMPDIR is used[default = None].
--compresslevel¶
Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default (which is 9)
profiling and debugging options¶
--timeit¶
Store timeing information in file [default=none].
--timeit-name¶
Name in timing file for this class of jobs [default=all].
--timeit-header¶
Add header for timing information [default=none].
--random-seed¶
Random seed to initialize number generator with [default=none].