TODO

==================
GLU 1.0+ TODO LIST
==================

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documentation
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  * Update installation documentation
  * Complete user reference guide
  * Complete user tutorial
  * Complete developer reference guide

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distribution
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  * ==DONE== Prepare Linux binary distribution (AMD64 and Intel64)
  * ==DONE== Prepare OSX binary distribution
  * ==DONE== Prepare win32 binary distribution (AMD and Intel)

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genolib
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  * Improve genoarray exceptions so they can be better distinguished and
    handled

  * File format auto-detection based on headers (HapMap, ldat, sdat, ?bat, primarily)

  * Add support for yet another WTCCC format: https://www.wtccc.org.uk/info/data_formats.shtml

  * Improve file format support:
    * PLINK text (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml)
    * PLINK binary (http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml)
    * MERLIN/MACH (http://www.sph.umich.edu/csg/abecasis/MACH/tour/)
    * GenABEL (http://rss.acs.unt.edu/Rdoc/library/GenABEL/html/GenABEL-package.html)
    * PHASE (http://stephenslab.uchicago.edu/instruct2.1.pdf)
    * STRUCTURE (http://pritch.bsd.uchicago.edu/software/structure22/readme.pdf)
    * WTCCC (http://www.stats.ox.ac.uk/%7Emarchini/software/gwas/file_format.html)


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modules.assoc
-------------

  * Optimize unadjusted models
  * Add ordinal logistic regression
  * Add support for MACH dosage and posterior genotype probability models
  * Add GLM for correlated data (Pete wants to look at Framingham)
  * Add user-level support for regression weights
  * Add robust variance estimator(s)