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Referee v1.1.21
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@gwct gwct released this 27 Sep 19:26
· 12 commits to master since this release
1.1.21
3222507

v1.1.21

  • Added maxmimum input file size of 100GB to input -gl files to prevent users from duplicating large files and having intractable run times.
  • 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.
  • Added an error message when trying to read .gz compressed FASTA reference file.

v1.1

  • Implemented the --haploid option to score genomes from haploid species. This option can only be used in conjunction with an input --pileup file as the likelihoods must be calculated internally. This restricts the possible genotype likelihoods to the four base states and only considers a single allele in the likelihood calculation. See: https://gwct.github.io/referee/calcs.html
  • Fixed the order of operations for the probability calculations with mapping quality.
  • Updated unichr to chr for Python 3.
  • (v1.1.1) 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.

To install

Referee does not need to be compiled. Simply download one of the source packages below, decompress, and run with python referee.py <options>. You may want to add the referee folder to you $PATH variable for ease of use.

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