AlphaImpute-docs README

This README file is not for AlphaImpute. This README file is for the AlphaImpute manuals.

Manuals are written in Markdown.

For printable editions, manuals are compiled using pandoc and LaTeX. Pandoc requires some additional extensions. pandoc-tablenos and pandoc-fignos for ennumerating figure and table captions.

Organization: / - scripts for compiling various versions of the manuals. /chapters/ - each chapter can be found as a separate file. /examples/ - examples used in the manuals, complete with input data and spec files. /figures/ - figures for manuals.

Numbering and referencing figures and tables

To set a caption for a table:

Table: Caption {#tbl:lbl} 

Table is mandatory (I believe). Curly brackets must appear at end.

To reference the table use @tbl:lbl.

To set a caption for a figure:

![Figure-caption](filename){#fig:lbl}

To reference the figure use @fig:lbl.

Installation:

Run python installers as root / administrator:

pip install pandoc-tablenos 
pip install pandoc-fignos

• pandoc-fignos: https://github.com/tomduck/pandoc-fignos
• pandoc-tablenos: https://github.com/tomduck/pandoc-tablenos