Version 1.4.0

  • Switched to conda install
  • Added continuous delivery

Version 1.3.2

  • fasta added –disambiguate option to turn ambiguous sequences into all permutations possible

Version 1.3.1

  • plot_muts added –cluster and –html options
  • fasta added –split and –wrap options

Version 1.3.0

  • Added fasta script that removes newlines from fasta sequences

Version 1.2.1

  • Fixed some python3 and python2.6 incompatability issues
  • Fixed some old bio_pieces references
  • Added some simple tests for plot_muts

Version 1.2.0

  • Renamed project to bio_bits to fix naming issue with other project
  • GPL License added
  • degen_regions script added
  • parallel_blast added
  • plot_muts script added

Version 1.1.0

  • Renamed parse_contigs to group_references to better name functionality
  • group_references now supports bam files

Version 1.0.0

  • Version bump. Starting here we will employ semantic versioning
  • Added version script to get version from project

Version 0.1.0

  • Started project over to setup for Continuous Integration testing
  • Added rename_fasta that can rename fasta sequence identifiers based on a input rename file
  • Added travis, coveralls, readthedocs
  • Added amos file parser that is specific to Ray assembler amos format
  • Added format functionality for amos classes such that it is easy to convert to different formats
  • Added amos2fastq to pull sequences out of AMOS files organized by their contigs.
  • Added, a commandline app for filtering and comparing vcf files.
  • Completed documentation for vcfcat
  • Added beast_checkpoint script and documentation
  • Added beast_wrapper script that prints estimated time column in beast output
  • Added beast_est_time script that allows you to easily get estimated time left from already running beast run