Stability fixes over Feldman. Includes:

• new config variable, BUCKET_SIZE, which can be scaled for different resolutions in map generation.
• links to example input and output in readme

Stable! Maps are generated for strains under most every condition, and readme has been updated to reflect usages in personal comparison.

updates to map maker

Bug fixes, better error reporting.

• Genome maps are made more reliably.
• Reports when no genes are present in >85% of strains.

New analysis option! Pipeline will generate maps of where on the concatenated genome recombination takes place. Files will be output in a maps folder.

New features:

• specify number of threads in personal comparison with -t #. This is the maximum number of threads used by the comparison process that is launched.
• generate maps in maps folder. Creates a genome map showing locations of recombination of every strain against every other strain in the population.
• specify the name of your BBH folder. Useful to rename the BBH folder to something that can be avoided by backup systems, such as tmp. Necessitated by the fact the output of USearch is the only n^2 file operation.

Better output management in personal comparison

Launches the newest feature: personal comparison specified via a command line argument rather than in the configuration.

Additional Fixes:

• specify in config.py how distant files can be before they are excluded (via RAxML distance ratings)
• fixed atomicity error in calc_hm that would sometimes produce corrupted rm1.txt files

Additionally, streamlines the Personal Comparison and Database Building versions of the pipeline to pull from a shared family of scripts, making future updates and bug fixes more effective and efficient. In that vein, this release now includes all scripts, even those not intended for general audiences. The READMEs will point to the bits that are important.

Extended flexibility in 'personal comparison' section to more accurately account for the variety of file variants within the FASTA format. Uses similar cleaning methods found in the web-server variant of Conspecifix.

Stable release of the ConSpecifFix pipeline with Personal Comparison and Database Building variants. Full installation instructions and required external software are listed in READMEs across the project.

almost got it: One last release before committing to calling it stable.