Change Log

This document follows guidelines from Keep a Changelog and adheres to semantic versioning.

[0.7.0] - 2019-08-15


  • Use command callability checker from ubiquerg.
  • Moved to logmuse, removing the logging functions from pararead


  • Fixed bug with example that prevented it from working on multiple cores

[0.6.0] - 2019-03-25

  • Made compatible with python 3

[0.5.0] - 2018-09-20


  • 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 runtime.
  • 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 and projects.