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-* GEMMA Design Document
-
-** Introduction
-
-With the v0.98 release GEMMA has stabilized and contains extensive
-error checking. To move faster we are moving towards integrating the
-faster-lmm-d code base which is written in the D programming
-language. We are also add interfaces for Python and R (and other
-languages). We will try to keep a legacy C++ based GEMMA as long as
-possible, but for performance and features it is likely a D compiler
-is required. The good news is that most distributions contain D
-compilers today.
-
-** Faster-lmm-d integration
-
-Faster-lmm-d is mostly a rewrite of GEMMA univariate LMM and
-multivariate LMM resolvers. We compile faster-lmm-d as a library that
-can be linked against GEMMA. For computing K, for example, there are
-two modes: (1) that has all genotype data in RAM and (2) that loads
-the genotype data directly from a geno file.
-
-** Improved data formats
-
-The original data formats are somewhat lacking because they make error
-correction hard. In collaboration with the R/qtl2 project we aim for
-supporting newer formats.
-
-*** Kinship format
-
-As the kinship mastrix K is symmetric we only need to store half the
-data. Also we want to be able to filter and validate on the names of
-individuals/samples. Next we compress it. A comparison of formats is
-[[https://catchchallenger.first-world.info/wiki/Quick_Benchmark:_Gzip_vs_Bzip2_vs_LZMA_vs_XZ_vs_LZ4_vs_LZO][here]]. Decompression speed is most critical and [[https://github.com/lz4/lz4][lz4]] does a great job
-there (lz4 is used in CRAM and sambamba). According to [[https://www.dummeraugust.com/main/content/blog/posts.php?pid=173][this comparison]]
-text processing is fairly similar between gzip and lz4. lz4 files are
-a bit larger, so decompression gains may be offset by network speeds.
-
-To recognise the tab dilimited file we'll add a header with nind's:
-
-#+BEGIN_SRC
-# GRMv1.0
-# nind=900
-ind1 0.1436717816 0.006341902008 0.007596806816 ...
-ind2 0.007996662028 0.008741860935 0.008489758779 ...
-...
-ind900 0.002311556029
-#+END_SRC
-
-where each row is one value shorter describing the right top half of
-K. This setup allows one to use a K with for exaple ind1 missing -
-just remove that row and column. The data will be stored as
-name.cXX.txt.lz4 (later add the alternative name.cxx.txt.gz).