Bugfix

Incorporate new argutils version that fixes a bug during 'swga init'

Refactoring, new features, and bugfixes

Features:

• Export primer binding evenness
• Calculated primer-level gini indices
• Bedgraph export now counts binding sites, not number of nucleotides bound
• Simplified install
• Checks to ensure swga version is compatible with workspace

Bugfixes:

• Many

Bugfixes

Myriad bugfixes

v0.3.6: Bugfixes

Mostly a bugfix release. This should fix some issues people have had with exports and also some random install problems.

Version 0.3.2: bugfixes and optimizations

Version 0.3.2

This update brings mostly bugfixes and a few small enhancements. The parameters file has been updated, so be sure to run swga init again on any current project.

What's new:

• swga init now prompts for an exclusionary FASTA file that will be used to
  prevent certain primers from being used (i.e. any primer that appears in the
  sequences given in the exclusionary file will be omitted).
• Bugfix: DSK does not include a primer's reverse complement in its list of
  primers counted. We've accounted for this as per issue #17.
• Bugfix: Locate functions now check for reverse complement, not just reverse
  (this may have a pretty large impact on your sets, so worth re-running any
  analyses with the update)
• Wiki has been organized and cleaned up
• Lots of usability enhancements from Sesh (thanks Sesh!)
• Other code cleanups and bugfixes

SWGA version 0.3.0 (Production)

This marks our first release suitable for widespread use.

New Features

• Totally revamped architecture based on a SQLite database for storing primers and sets
• K-mer counting has now been integrated into the pipeline, so you can just start from your two genomes and nothing else
• Melt temp calculations are now integrated and super accurate: can account for mono- and divalent cation concentrations correctly
• Major workflow improvements:
  • Now only three basic commands: count, filter, and find sets
  • Cool helper commands like:
    • swga init that makes a config file for you with pre-filled defaults,
    • swga summary that tells you how many primers you have, their average binding frequencies, melting temps, and stats about the best set you’ve found so far, and
    • swga setopt that changes a value in your config file for you automatically.
  • Way better export function (swga export) that lets you do things like:
    • Export your best sets to excel/tab-delimited format, bed format, or bedgraph format
    • Export all your primers and their stats to tab-delimited format
    • Order and export primers and sets based on various criteria, like binding ratio, score, evenness, and more
    • Visualize statistics right on the command line
  • Ability to exclude any primers that bind anywhere in a given FASTA file
  • Ability to only feed in selected lists of primers instead of counting all the kmers from scratch
• Super-easy installation process that doesn’t require root
• Helpful new wiki: (https://github.com/eclarke/swga/wiki)
• Colorful output!
• Lots of bug fixes
• Continuous code quality testing using Travis CI

Beta Release

Beta release (usable for testing, but likely extensive issues).

Major features:

• User-definable scoring expression
• User-definable scoring/set processing function plugin
• Usability and syntax improvements
• Major bugfixes
• Improved pipeline output
• Better documentation

Major things not yet implemented

• Specify list of primers to exclude
• Integrate kmer-counting functions
• Flexibility when analyzing custom sets

Alpha release

The business logic should be mostly intact. Unfinished: documentation, flexible set statistics, bug hunting