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 d, dprime-signed Jul 31, 2016
.gitignore save failed copy_bitarr_subset experiment Jan 9, 2016
LICENSE add GPL Jul 22, 2012
Makefile update Makefile Jan 17, 2017
Makefile.std update Makefile Jan 17, 2017
README.md readme edit Nov 23, 2015
Rconnection.cc prettify 2x3 chi-square zero result Jan 10, 2016
Rconnection.h deal with clang warnings Jan 7, 2016
Rsrv.h oops, forgot to add new files Jan 17, 2015
SFMT.c unbreak 32-bit compilation; collapse_copy_quaterarr_incl upgrade, part 1 Jan 9, 2016
SFMT.h explicitly include SFMT license in source code Jun 25, 2013
bgen_to_gen.c upgrade to zlib 1.2.10? (hey, it's already lasted twice as long as 1.… Jan 6, 2017
bgzf.c move _FILE_OFFSET_BITS=64 to safer place Sep 15, 2016
bgzf.h initial --recode vcf bgz implementation Feb 7, 2015
config.h oops, forgot to add config.h to repo Jan 20, 2015
dbl2txt.c start debugging dprime Dec 3, 2013
dcdflib.c attempt #4: copy older libc onto EC2 instance Apr 2, 2014
dcdflib.h --linear set-test working Dec 6, 2014
dose2plink.c update zlib include directory in .h/.c files. (will soon be time to m… Jan 6, 2017
hfile.c deal with clang warnings Jan 7, 2016
hfile.h initial --recode vcf bgz implementation Feb 7, 2015
hfile_internal.h initial --recode vcf bgz implementation Feb 7, 2015
hts.h remove socket.h dependency to simplify Windows compilation, add forgo… Feb 7, 2015
hts_defs.h initial --recode vcf bgz implementation Feb 7, 2015
interval_merge.c --annotate command line parsing, nsort.c, interval_merge.c May 26, 2014
ipmpar.h basic --assoc/--fisher working Feb 15, 2013
khash.h deal with clang warnings Jan 7, 2016
nsort.c --annotate command line parsing, nsort.c, interval_merge.c May 26, 2014
pigz.c zlib 1.2.10 -> 1.2.11, but automatically fall back on /fossils if ini… Jan 17, 2017
pigz.h make --dosage Zout support multithreaded compression Feb 15, 2015
plink.c zlib 1.2.10 -> 1.2.11, but automatically fall back on /fossils if ini… Jan 17, 2017
plink_assoc.c fix --ld-snps Jan 13, 2017
plink_assoc.h fix --ld-snps Jan 13, 2017
plink_calc.c fix --ld-snps Jan 13, 2017
plink_calc.h rename global wkspace to g_bigstack, make allocators a bit safer Dec 26, 2015
plink_cluster.c fix --ld-snps Jan 13, 2017
plink_cluster.h replicate old --dosage 0.01 <= FRQ <= 0.99 and 0.1 <= INFO <= 2.0 res… Dec 2, 2015
plink_cnv.c fix --ld-snps Jan 13, 2017
plink_cnv.h fix --ld-snps Jan 13, 2017
plink_common.c fix --ld-snps Jan 13, 2017
plink_common.h zlib 1.2.10 -> 1.2.11, but automatically fall back on /fossils if ini… Jan 17, 2017
plink_data.c fix --ld-snps Jan 13, 2017
plink_data.h fix --ld-snps Jan 13, 2017
plink_dosage.c fix --ld-snps Jan 13, 2017
plink_dosage.h fix --ld-snps Jan 13, 2017
plink_family.c fix --ld-snps Jan 13, 2017
plink_family.h fix --ld-snps Jan 13, 2017
plink_filter.c fix --ld-snps Jan 13, 2017
plink_filter.h fix --ld-snps Jan 13, 2017
plink_first_compile zlib 1.2.10 -> 1.2.11, but automatically fall back on /fossils if ini… Jan 17, 2017
plink_glm.c fix --ld-snps Jan 13, 2017
plink_glm.h fix --ld-snps Jan 13, 2017
plink_help.c fix --ld-snps Jan 13, 2017
plink_help.h fix --ld-snps Jan 13, 2017
plink_homozyg.c fix --ld-snps Jan 13, 2017
plink_homozyg.h fix --ld-snps Jan 13, 2017
plink_lasso.c fix --ld-snps Jan 13, 2017
plink_lasso.h fix --ld-snps Jan 13, 2017
plink_ld.c fix --ld-snps Jan 13, 2017
plink_ld.h fix --ld-snps Jan 13, 2017
plink_matrix.c fix --ld-snps Jan 13, 2017
plink_matrix.h fix --ld-snps Jan 13, 2017
plink_misc.c fix --ld-snps Jan 13, 2017
plink_misc.h fix --ld-snps Jan 13, 2017
plink_perm.c fix --ld-snps Jan 13, 2017
plink_perm.h fix --ld-snps Jan 13, 2017
plink_rserve.c fix --ld-snps Jan 13, 2017
plink_rserve.h fix --ld-snps Jan 13, 2017
plink_set.c fix --ld-snps Jan 13, 2017
plink_set.h fix --ld-snps Jan 13, 2017
plink_stats.c fix --ld-snps Jan 13, 2017
plink_stats.h fix --ld-snps Jan 13, 2017
prettify.c dose2plink, 1-pass Nov 9, 2014
sisocks.h oops, forgot to add new files Jan 17, 2015
toy.map .bim stub working Dec 31, 2012
toy.ped regularize toy.ped Jan 28, 2013
yarn.c rename Rconnection.cc to Rconnection.c so __cplusplus can be used to … Dec 23, 2015
yarn.h pzwrite interface Feb 9, 2015

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 .