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.