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Change Log

All notable changes to Rp-Bp will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.1.7] - 2017-04-03

Fixed

  • Incorrect alignment of ORF data frame and profile matrix. See Issue #54 for more details.
  • ORF coordinates for start codon on exon boundary. See Issue #64 after the reopening for more details.

[1.1.6] - 2017-03-31

Updated

  • Predictions report formatting
  • Guessing read filtering plot tick marks. See Issue #60 for details.

Fixed

  • ORF coordinates when start and stop codons fall on an exon boundary. See Issue #64 for more details.

[1.1.5] - 2017-03-29

Added

  • Documentation for the analysis scripts
  • Documentation for creating reference indices

Fixed

  • Checks that annotation files exist before beginning index creation. See Issue #62
  • Remove unnecessary --tmp argument for pipeline call to predict-translated-orfs. See Issue #63 for more details.

[1.1.4] - 2017-02-22

Removed

  • Unnecessary [analysis] package. Depending on how the package was installed, this sometimes resulted in the scripts not being found. See [Issue #56] (dieterich-lab#56) for details.

[1.1.3] - 2017-02-21

Fixed

  • Handling of Stan model paths which include spaces. See Issue #36 for more details. This bug was reintroduced with the commit: "UPD resolve conflicts from dev for version 1.1"

[1.1.2] - 2017-02-15

Fixed

  • Backward-compatiblity syntax in estimate-orf-bayes-factors. See Issue #51 for more details.

Added

  • __version__ and __version_info__ for rpbp package

[1.1.1] - 2017-02-14

Updated

  • Documentation to use pandoc for converting markdown to html

Fixed

  • Broken download link to example files

[1.1.0] - 2017-02-14

This is a rather significant update to the codebase and includes many small changes. Primarily, though, it addresses many installation and system issues.

In particular, thanks to Tonu Margus (@tmargus) for working through many of these issues.

Added

  • Installation instructions for anaconda

Fixed

  • Various installation issues related to calling pip3 from setup.py. Installation of private repositories is now handled via a requirements.txt file.

Removed

  • All uses of (py)bedtools

[1.0.1] - 2017-02-01

Fixed

  • Handling of Stan model paths which include spaces. In particular, this was a problem on OSX. See Issue #36 for more details.

[1.0.0] - 2016-09-05

The initial version, which implements everything in the paper. It was only used on debian-based systems.