Added retain_temp argument that is useful for debugging.
Added modified version of read counting example to demonstrate logging.
Updated the CLI for logging options
[0.4.0] - 2018-02-27
Updated packaging and documentation for release on pypi.
[0.3.0] - 2017-06-09
A ParaReadProcessor's __call__ function is no longer applied to any
chromosome that's empty (i.e., to which no reads mapped). Instead, an action
(empty_action, which may be overridden) is taken for such a chromosome.
This frees an implementor of ParaReadProcessor from the need to worry about
empty chromosomes while allowing the flexibility for custom action in that case.
[0.2.0] - 2017-06-09
The read processor's constructor now establishes a root logger if that's
not already been done by a client application.
API functions to the logs module that assist clients in providing and
parsing logging options, and with integrating and using a logging system
in their applications.
Previously, an attempt was made to optimize distribution of read chunks
(e.g., by chromosome) by interleaving the read chunk keys (e.g., chromosome
names) according to the genomic size (in base pairs) of the chromosome. This
behavior is now turned off by default, as doing so seems to accelerate real
The name for the function with which to fetch a file that's been registered
with pararead changes from fetch to the clearer fetch_file, to
distinguish this from a function that, say, fetches a block of reads or
genomic positions/regions from a file.
Simplified use of more information-rich development mode in logging system.
The name for the function to create and configure a logger changes from
setup_pararead_logger to the more general setup_logger to reflect the
intention for this to serve as a common infrastructure for other repositories
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