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Added zsh completions into project root directory #2

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37 changes: 37 additions & 0 deletions .relate_completion.zsh
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# To deploy these completions you must
# make an alias for relate by adding to ~/.zshrc:
#
# alias relate='/path/to/relate/bin/Relate'
#
# and then copy and paste this script to the bottom of ~/.zshrc with:
#
# cat .relate_completion.zsh >> ~/.zshrc

autoload -U compinit; compinit
function _relate(){
_describe 'command' "(\
'--mode:Choose which part of the algorithm to run.' \
'--haps:Filename of the haps file (Output file format of Shapeit).'\
'--sample:Filename of the sample file (Output file format of Shapeit).'\
'--map:Genetic map.'\
'--mutation_rate:Mutation rate.'\
'--effectiveN:Effective population size.'\
'--output:Filename of outputu without file extension.'\
'--dist:Optional but recommended. Distance in BP \nbetween SNPs. Can be generated using RelateFileFormats. If unspecified, distances in haps are used.'\
'--annot:Optional. Filename of file containing additional annotation of snps. Can be generated using RelateFileFormats.'\
'--memory:Optional. Approximate memory allowance in GB for storing distance matrices. Default is 5GB.'\
'--sample_ages:Optional. Filename of file containing sample ages (one per line).'\
'--chunk_index:Optional. Index of chunk. (Use when running parts of the algorithm on an individual chunk).'\
'--first_section:Optional. Index of first section to infer. (Use when running parts of algorithm on an individual chunk.'\
'--last_section:Optional. Index of last section to infer. (Use when running parts of algorithm on an individual chunk.'\
'--coal:Optional. Filename of file containing coalescent rates. If specified, it will overwrite --effectiveN.'\
'--transversion:Only use transversion for bl estimation.'\
'--input:Filename of input'\
'--painting:Optional. Copying and transition parameters in chromosome painting algorithm. Format: theta, rho. Default: 0.025, 1.'\
'--seed:Optional. Seed for MCMC im branch lengths estimation.'\
)"

}

compdef _relate relate
setopt complete_aliases