A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).
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tests
.gitignore
LICENSE
Makefile
Makefile.std
README.md
Rconnection.cc
Rconnection.h
Rsrv.h
SFMT.c
SFMT.h
bgen_to_gen.c
bgzf.c
bgzf.h
config.h
dbl2txt.c
dcdflib.c
dcdflib.h
dose2plink.c
hfile.c
hfile.h
hfile_internal.h
hts.h
hts_defs.h
interval_merge.c
ipmpar.h
khash.h
nsort.c
pigz.c
pigz.h
plink.c
plink_assoc.c
plink_assoc.h
plink_calc.c
plink_calc.h
plink_cluster.c
plink_cluster.h
plink_cnv.c
plink_cnv.h
plink_common.c
plink_common.h
plink_data.c
plink_data.h
plink_dosage.c
plink_dosage.h
plink_family.c
plink_family.h
plink_filter.c
plink_filter.h
plink_first_compile
plink_for_UPPMAX.md
plink_glm.c
plink_glm.h
plink_help.c
plink_help.h
plink_homozyg.c
plink_homozyg.h
plink_lasso.c
plink_lasso.h
plink_ld.c
plink_ld.h
plink_matrix.c
plink_matrix.h
plink_misc.c
plink_misc.h
plink_perm.c
plink_perm.h
plink_rserve.c
plink_rserve.h
plink_set.c
plink_set.h
plink_stats.c
plink_stats.h
prettify.c
sisocks.h
toy.map
toy.ped
yarn.c
yarn.h

README.md

plink-ng

This is mostly a large collection of report-generating functions which do not depend on each other. plink_common contains convenience functions for file parsing and bit manipulation, plink_matrix encapsulates a few common matrix operations (which are resolved via LAPACK calls under the hood), and plink.c handles command-line parsing and initial dispatch; it's often not necessary to deal with any other files when adding a new command.

When building directly from the code in this repository, you'll probably want to use Makefile.std instead of Makefile; the latter is just aimed at my own OS X and Win64 machines.

Yes, I would like to migrate this codebase to C++11. Unfortunately, the version of GCC currently bundled with Scientific Linux, which we need to build maximally portable Linux binaries, has poor support for it.

Additional discussion is at https://www.cog-genomics.org/plink2/dev .