.gitignore
.gitmodules
.travis.yml
LICENSE
MANIFEST.in
Makefile
README.md
README.rst
_dEploid_demo.py
appveyor.yml
dEploid-py.cpp
dEploid_demo.py
lib
requirements.txt
setup.py
version
.circleci/config.yml
dEploid/__init__.py
dEploid/mcmc.py
dEploid/vcf.py
dEploid.egg-info/PKG-INFO
dEploid.egg-info/SOURCES.txt
dEploid.egg-info/dependency_links.txt
dEploid.egg-info/top_level.txt
docs/Bug-report.md
docs/Citing-DEploid.md
docs/Makefile
docs/conf.py
docs/description.rst
docs/index.rst
docs/installation.rst
docs/mcmc.rst
docs/modules.rst
docs/vcf.rst
docs/_static/deploidTransLow.png
docs/_static/deploidTransLowSmall.ico
docs/_static/mixedInfection.png
inst/extdata/deploid.png
lib/src/dEploidIO.cpp
lib/src/dEploidIO.hpp
lib/src/exceptions.hpp
lib/src/global.hpp
lib/src/ibd.cpp
lib/src/ibd.hpp
lib/src/mcmc.cpp
lib/src/mcmc.hpp
lib/src/panel.cpp
lib/src/panel.hpp
lib/src/txtReader.cpp
lib/src/txtReader.hpp
lib/src/updateHap.cpp
lib/src/updateHap.hpp
lib/src/utility.cpp
lib/src/utility.hpp
lib/src/variantIndex.cpp
lib/src/variantIndex.hpp
lib/src/vcfReader.cpp
lib/src/vcfReader.hpp
lib/src/codeCogs/asympt_expn.h
lib/src/codeCogs/errorfn.h
lib/src/codeCogs/errorfnc.h
lib/src/codeCogs/errorfnc_exp.h
lib/src/codeCogs/expx2.h
lib/src/codeCogs/gamma.h
lib/src/codeCogs/ln_add1.h
lib/src/codeCogs/log_gamma.h
lib/src/codeCogs/logbeta.h
lib/src/codeCogs/loggammafrac.h
lib/src/codeCogs/loggammasum.h
lib/src/codeCogs/machine_epsilon.h
lib/src/codeCogs/mersenne.hpp
lib/src/codeCogs/poly_eval.h
lib/src/codeCogs/randomSample.hpp
lib/src/codeCogs/stirling.h
lib/src/codeCogs/xsub_ln_add1.h
lib/src/debug/mcmcDebug.cpp
lib/src/debug/vcfReaderDebug.cpp
lib/src/export/dEploidIOExport.cpp
lib/src/export/dEploidIOExportPosteriorProb.cpp
lib/src/export/writeMcmcRelated.cpp
lib/src/gzstream/gzstream.cpp
lib/src/gzstream/gzstream.h
lib/src/lasso/src/dEploidLasso.cpp
lib/src/lasso/src/dEploidLasso.hpp
lib/src/lasso/src/dbgmacro.hpp
lib/src/lasso/src/lasso.cpp
lib/src/lasso/src/lasso.hpp
lib/src/lasso/src/lassoDBG.cpp
lib/src/random/fastfunc.cpp
lib/src/random/fastfunc.hpp
lib/src/random/mersenne_twister.cpp
lib/src/random/mersenne_twister.hpp
lib/src/random/random_generator.cpp
lib/src/random/random_generator.hpp