This document follows guidelines from Keep a Changelog and adheres to semantic versioning.
retain_temp argument that is useful for debugging.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.logs module that assist clients in providing and
parsing logging options, and with integrating and using a logging system
in their applications.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.setup_pararead_logger to the more general setup_logger to reflect the
intention for this to serve as a common infrastructure for other repositories
and projects.