Caltha 0.6

Version 0.6

Current stable version. Previous versions should be ignored.

• Add pytest file presence test function for regular fastq file input.
• Add pytest file presence test function for gzipped fastq file input.
• Add pytest file presence test function for regular fasta file input.
• Re-add pytest test file with file presence test for gzipped fasta
  file input (further tests will be added later).
• Remove both the umi sequence and the centroid sequence from the tabular
  output, as requested by users and noted in
  (issue 7)[https://github.com//issues/7].
• Fix fasta file creation, where new read headers would not start on a
  new line, but append to the sequence of the previous read.
• Rename PreZip folders and files to PreValidation.
• Fix bug where umi count would be reset to 1 for every read.
• Replace reverse complement function with the biopython Seq class.
• Add pyfastx for the parsing of the fasta/fastq files (which also adds
  support for single gzipped input files or multiple gzipped files in a zip
  archive).
• Update documented python version to 3.8.
• Rename variables in core script and update Caltha --help page.
• Update README.md & index.md to reflect current project state.
• Fix pre-commit files.

Caltha 0.5.1

Version 0.5.1

• Restructure versioning to match PyPI package.

Caltha 0.5

Version 0.5

• Setup pre-commit with Black and Flake8.

Caltha 0.4

Version 0.4

• Add code style Black.

Caltha 0.3

Version 0.3

• Updated python script for umi5 primer single test to work with parallel
  processing.
• Added zip file for umi5 primer multiple test.

Caltha 0.2

Version 0.2

This release of Caltha implements parallel processing. This parallel
processing only has effect when multiple input files are provided. Caltha now
allows a .zip file with either fasta or fastq files as input. The output has
been changed to three zip files, one for the tabular files, one for the pre
validation zip files and one for blast files.

• Added parallel processing issue #2.
• Added .travis.yml configuration file.

Caltha 0.1.3

Version 0.1.3

• Added python script for umi5 primer single test.

Caltha 0.1.2

Version 0.1.2

• Added fasta file for umi5 primer single test.

Caltha 0.1.1

Version 0.1.1

• Implemented a umi length check.

Caltha 0.1

Version 0.1

First release on GitHub for the new Caltha tool.
Any changes mentioned below were applied to the main python script after it was
isolated from the old "galaxy-tools-umi-isolation" repository. This python
script is now a package on PyPI and will be maintained in this repository.

• Created PyPI package for Caltha.
• Added documentation page to repository (still needs to be filled).
• Zip archives are now created
  by Caltha (used to be created by a BASH script).
• Temporary working directories are now managed by Caltha (used to be managed
  by a BASH script).
• Wrongly assigned reads bug was
  fixed (PR by https://github.com/dickgroenenberg).
• Renamed galaxy-tools-umi-isolation python tool to Caltha.
• Isolated galaxy-tools-umi-isolation python script to dedicated repository.