CHANGELOG.txt

# These are the major changes and updates. For build specific changes (which are too numerous to document manually), check the commits on github.

# TODO:
1) Implement a check for headers in external genotype likelihood files such that if headers aren't present in the right order, the program exits and tells the user to add them.
2) Improve the multiprocessing procedure such that 1) the input file is read through only once and 2) duplicates of the input file are not created.

# DEVELOPMENT:


# CURRENT:
# Version 1.1.2: September 27, 2019
01) Added and error message when trying to read .gz compressed FASTA reference file.
02) Added maxmimum input file size of 100GB to input -gl files to prevent users from duplicating large files and having intractable run times.
03) Added the bam_split.sh and tab_split.sh helper scripts to aid users that need to split large BAM, pileup, or ANGSD files by scaffold.

# PREVIOUS:
# Version 1.1.1: September 24, 2019
01) Fixed a bug where all scores output would be -2 after encountering a site with no reads mapped in a pileup file. Thanks to @reedacartwright.

# Version 1.1: August 31, 2019
01) Implemented the --haploid option to score genomes from haploid species.
02) Fixed the order of operations for the probability calcs with mapping quality.
03) Updated unichr to chr for python 3.

# Version 1.0: April 18, 2019
01) First official release coincides with publication. No major changes, cleaned up repository.

# Version Beta 1.2: November 4, 2018
01) Added --bed option for output to BED files.
02) Redesigned the website

# Version Beta 1.1: October 14, 2018
01) Implemented in-house genotype likelihood calculations with --pileup input.
02) Added the website.

# Version Beta 1.0: October 6, 2018
01)	First commit and implementation of reference quality algorithm.