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].


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].


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)

profiling and debugging options


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].