limix/bgen

A BGEN file format reader.

limix

Genomic analyses require flexible models that can be adapted to the needs of the user.

Limix is a flexible and efficient linear mixed model library with interfaces to Python. It includes methods for

• Single-variant association and interaction testing
• Variance decompostion analysis with linear mixed models
• Association and interaction set tests
• Different utils for statistical analysis, basic i/o, and plotting.

We have an extensive documentation of the library. If you need further help or want to discuss anything related to limix, please, join our forum 💬 and have a chat with us 😃. In case you have found a bug, please, report it creating an issue.

Install

NOTE: We will be maintaining limix 2.0.x for a while, in case you find some missing feature in limix 3.0.x. If that is the case, please, type pip install "limix <3,>=2" in your terminal.

Installation is easy and works on macOS, Linux, and Windows:

pip install limix

If you already have Limix but want to upgrade it to the latest version:

pip install limix --upgrade

Interactive tutorials

• eQTL (requires limix 2.0.x)
• Struct-LMM (requires limix 2.0.x)

Running tests

After installation, you can test it

python -c "import limix; limix.test()"

as long as you have pytest.

Authors

• Christoph Lippert
• Danilo Horta
• Francesco Paolo Casale
• Oliver Stegle

License

This project is licensed under the Apache License License.

bgen's Issues

On Windows Git Bash, bgen build fails all tests

Here is the log. The internet suggests that xc0000135 might be a missing DLL, but I don't how to learn which one. Thanks!

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   117  100   117    0     0    433      0 --:--:-- --:--:-- --:--:--   433

 43 5398k   43 2353k    0     0  2264k      0  0:00:02  0:00:01  0:00:01 2264k
100 5398k  100 5398k    0     0  3889k      0  0:00:01  0:00:01 --:--:-- 8750k
-- Building for: Visual Studio 16 2019
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.17/Modules/GNUInstallDirs.cmake:225 (message):
  Unable to determine default CMAKE_INSTALL_LIBDIR directory because no
  target architecture is known.  Please enable at least one language before
  including GNUInstallDirs.
Call Stack (most recent call first):
  cmake/limix.cmake:9 (include)
  CMakeLists.txt:2 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-------------------------------------------------------------------------------
Hello there. This is the bgen (3.0.3) project. We wish you an easy ride.
If by any chance you find in trouble, please, do not hesitate in contacting
us at <https://github.com/limix/bgen/issues/new>.
-------------------------------------------------------------------------------
-- Selecting Windows SDK version 10.0.17763.0 to target Windows 10.0.18363.
-- The C compiler identification is MSVC 19.24.28316.0
-- Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Tools/MSVC/14.24.28314/bin/Hostx64/x64/cl.exe
-- Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Tools/MSVC/14.24.28314/bin/Hostx64/x64/cl.exe - works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found ZLIB: C:/Program Files/zlib/lib/zlib.lib (found version "1.2.11") 
-- Found ZSTD: C:/Program Files/zstd/lib/zstd.lib  
-- Found ATHR: C:/Program Files/athr/lib/ATHR.LIB  
-- Configuring done
-- Generating done
-- Build files have been written to: M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/build
Microsoft (R) Build Engine version 16.4.0+e901037fe for .NET Framework
Copyright (C) Microsoft Corporation. All rights reserved.

C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\ZERO_CHECK.vcxproj]
  Checking Build System
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/CMakeLists.txt
  buffer.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\depr\buffer.c(180,1): warning C4267: 'initializing': conversion from 'size_t' to 'long', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
  variants_index.c
  geno.c
  index.c
  io.c
  one.c
  two.c
  metafile.c
  str.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\str.c(31,21): warning C4244: 'function': conversion from 'uint64_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
  zlib.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\zip\zlib.c(52,1): warning C4267: 'initializing': conversion from 'size_t' to 'uInt', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
  zstd.c
  mmap.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\win\mmap.c(58,47): warning C4013: '_get_osfhandle' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\win\mmap.c(58,51): warning C4312: 'type cast': conversion from 'int' to 'HANDLE' of greater size [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
  Generating Code...
  tpl.c
  variant.c
  file.c
  file.c
  tpl.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(317,52): warning C4244: '=': conversion from 'uintptr_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(624,37): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(627,10): warning C4013: 'close' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(939,57): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1069,30): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1072,31): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1084,23): warning C4013: 'write' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1094,25): warning C4013: '_chsize' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1153,14): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1185,49): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1453,37): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1468,43): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1518,57): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1874,15): warning C4013: '_open' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1882,22): warning C4267: 'function': conversion from 'size_t' to 'unsigned int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1890,24): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1902,23): warning C4013: 'open' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2009,55): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2400,18): warning C4013: 'read' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2558,36): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2567,48): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2652,28): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2661,40): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen.vcxproj]
  variant.c
     Creating library M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/build/Release/bgen.lib and object M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/build/Release/bgen.exp
  bgen.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\Release\bgen.dll
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/CMakeLists.txt
  buffer.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\depr\buffer.c(180,1): warning C4267: 'initializing': conversion from 'size_t' to 'long', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
  variants_index.c
  geno.c
  index.c
  io.c
  one.c
  two.c
  metafile.c
  str.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\str.c(31,21): warning C4244: 'function': conversion from 'uint64_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
  zlib.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\zip\zlib.c(52,1): warning C4267: 'initializing': conversion from 'size_t' to 'uInt', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
  zstd.c
  mmap.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\win\mmap.c(58,47): warning C4013: '_get_osfhandle' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\win\mmap.c(58,51): warning C4312: 'type cast': conversion from 'int' to 'HANDLE' of greater size [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
  Generating Code...
  tpl.c
  variant.c
  file.c
  file.c
  tpl.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(317,52): warning C4244: '=': conversion from 'uintptr_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(624,37): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(627,10): warning C4013: 'close' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(939,57): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1069,30): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1072,31): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1084,23): warning C4013: 'write' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1094,25): warning C4013: '_chsize' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1153,14): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1185,49): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1453,37): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1468,43): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1518,57): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1874,15): warning C4013: '_open' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1882,22): warning C4267: 'function': conversion from 'size_t' to 'unsigned int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1890,24): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(1902,23): warning C4013: 'open' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2009,55): warning C4267: '=': conversion from 'size_t' to 'uint32_t', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2400,18): warning C4013: 'read' undefined; assuming extern returning int [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2558,36): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2567,48): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2652,28): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\src\tpl\tpl.c(2661,40): warning C4267: '=': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\bgen_static.vcxproj]
  variant.c
  bgen_static.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\Release\bgen_static.lib
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_2.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  assert_interface_2.c
  test_assert_interface_2.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_assert_interface_2.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  assert_interface_3.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\assert_interface_3.c(120,17): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\assert_interface_3.c(121,17): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3.vcxproj]
  test_assert_interface_3.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_assert_interface_3.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3_complex.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  assert_interface_3_complex.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\assert_interface_3_complex.c(50,9): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3_complex.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\assert_interface_3_complex.c(51,9): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3_complex.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\assert_interface_3_complex.c(123,55): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3_complex.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\assert_interface_3_complex.c(131,17): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3_complex.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\assert_interface_3_complex.c(132,17): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_assert_interface_3_complex.vcxproj]
  test_assert_interface_3_complex.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_assert_interface_3_complex.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_complex.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  complex.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\complex.c(149,49): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_complex.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\complex.c(152,35): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_complex.vcxproj]
  test_complex.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_complex.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_haplotype.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  haplotype.c
  test_haplotype.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_haplotype.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_index.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  index.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\index.c(33,1): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_index.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\index.c(40,1): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_index.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\index.c(43,1): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_index.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\index.c(47,1): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_index.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\index.c(50,1): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_index.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\index.c(53,1): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_index.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\index.c(57,1): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_index.vcxproj]
  test_index.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_index.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_metadata_example.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  metadata_example.c
  test_metadata_example.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_metadata_example.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_open_genotype.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  open_genotype.c
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\open_genotype.c(133,39): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_open_genotype.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\open_genotype.c(194,39): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_open_genotype.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\open_genotype.c(204,53): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_open_genotype.vcxproj]
M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\test\open_genotype.c(207,39): warning C4267: 'function': conversion from 'size_t' to 'int', possible loss of data [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_open_genotype.vcxproj]
  test_open_genotype.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_open_genotype.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_pbgen_example.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  pbgen_example.c
  test_pbgen_example.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_pbgen_example.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_v12_zlib_layout2.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  v12_zlib_layout2.c
  example_files.c
  Generating Code...
  test_v12_zlib_layout2.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_v12_zlib_layout2.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\test_zero_len_chrom_id.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/test/CMakeLists.txt
  zero_len_chrom_id.c
  test_zero_len_chrom_id.vcxproj -> M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\test\Release\test_zero_len_chrom_id.exe
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Microsoft\VC\v160\Microsoft.CppBuild.targets(467,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [M:\Temp\carl\tmp.ZIbhua79Djbgen\bgen-3.0.3\build\ALL_BUILD.vcxproj]
  Building Custom Rule M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/CMakeLists.txt
Test project M:/Temp/carl/tmp.ZIbhua79Djbgen/bgen-3.0.3/build
      Start  1: test_v12_zlib_layout2
 1/11 Test  #1: test_v12_zlib_layout2 .............Exit code 0xc0000135
***Exception:   0.04 sec

      Start  2: test_zero_len_chrom_id
 2/11 Test  #2: test_zero_len_chrom_id ............Exit code 0xc0000135
***Exception:   0.03 sec

      Start  3: test_pbgen_example
 3/11 Test  #3: test_pbgen_example ................Exit code 0xc0000135
***Exception:   0.02 sec

      Start  4: test_metadata_example
 4/11 Test  #4: test_metadata_example .............Exit code 0xc0000135
***Exception:   0.02 sec

      Start  5: test_haplotype
 5/11 Test  #5: test_haplotype ....................Exit code 0xc0000135
***Exception:   0.02 sec

      Start  6: test_complex
 6/11 Test  #6: test_complex ......................Exit code 0xc0000135
***Exception:   0.02 sec

      Start  7: test_index
 7/11 Test  #7: test_index ........................Exit code 0xc0000135
***Exception:   0.02 sec

      Start  8: test_open_genotype
 8/11 Test  #8: test_open_genotype ................Exit code 0xc0000135
***Exception:   0.02 sec

      Start  9: test_assert_interface_2
 9/11 Test  #9: test_assert_interface_2 ...........Exit code 0xc0000135
***Exception:   0.02 sec

      Start 10: test_assert_interface_3
10/11 Test #10: test_assert_interface_3 ...........Exit code 0xc0000135
***Exception:   0.02 sec

      Start 11: test_assert_interface_3_complex
11/11 Test #11: test_assert_interface_3_complex ...Exit code 0xc0000135
***Exception:   0.02 sec


0% tests passed, 11 tests failed out of 11

Total Test time (real) =   0.34 sec

The following tests FAILED:
	  1 - test_v12_zlib_layout2 (Exit code 0xc0000135
)
	  2 - test_zero_len_chrom_id (Exit code 0xc0000135
)
	  3 - test_pbgen_example (Exit code 0xc0000135
)
	  4 - test_metadata_example (Exit code 0xc0000135
)
	  5 - test_haplotype (Exit code 0xc0000135
)
	  6 - test_complex (Exit code 0xc0000135
)
	  7 - test_index (Exit code 0xc0000135
)
	  8 - test_open_genotype (Exit code 0xc0000135
)
	  9 - test_assert_interface_2 (Exit code 0xc0000135
)
	 10 - test_assert_interface_3 (Exit code 0xc0000135
)
	 11 - test_assert_interface_3_complex (Exit code 0xc0000135
)
Errors while running CTest

Plink filtered bgen files

@fpcasale could not import bgen files that have had SNPs filtered out by plink. (example files in the e-mail)

Checking bgen file with bgenix, running across the issue

Before using python (bgen_reader), I want to check the integrity of the data. (I downloaded a shared large dataset(~50G) by wget. namely, gwas_c20_b0_v3.bgen)

Do you have any clue about this? Thanks so much.

bgenix -g gwas_c20_b0_v3.bgen

Welcome to bgenix
(version: 1.1.7, revision )

(C) 2009-2017 University of Oxford

terminate called after throwing an instance of 'std::length_error'
what(): vector::_M_default_append
Aborted (core dumped)

compiling without network access

Hi, I'm trying to package bgen (and then python cbgen) in guix.
The trick is that guix does not permit network access during build so the cpmaddpackage commands do not work.
I've noticed it also comes in the dependency almosthere.

So the idea is package every dependency independently, and use those libraries for compiling.

My question is this, how do you compile your projects with local libraries located on the system.

NB: I am not well versed in C compilation
Thanks

On Windows, CMake complains that "warning" is not in any export set

Greetings,

When I try to "cmake ." (or use Visual Studio's Generate Cache on CMakeLists.txt), I get this error message:

Error CMake Error: install(EXPORT "bgen-targets" ...) includes target "bgen" which requires target "warning" that is not in any export set.

I see there is extra metacode in CMakeLists.txt about the warning interface and Windows (below), but I don't understand Cmake well enough to understand or debug it.

add_library(warning INTERFACE)
add_library(BGEN::warning ALIAS warning)
target_compile_options(warning INTERFACE
    $<$<STREQUAL:${CMAKE_C_COMPILER_ID},MSVC>:/W3>
    $<$<NOT:$<STREQUAL:${CMAKE_C_COMPILER_ID},MSVC>>:-Wall -Wextra -pedantic
    -Wstrict-prototypes -Wshadow -Wconversion -Wmissing-prototypes
    -Wno-unused-parameter -Wsign-conversion>

Thanks,

• Carl

'curl' build on Ubuntu fails with athr_export.h: No such file or directory

Greetings,
When I try to build via the curl command on Ubuntu (under Windows), I get a messing header message.

(base) carlk@kadie2:/mnt/d/OneDrive/programs/bgen-reader-py2$ curl -fsSL https://git.io/JerYI | GITHUB_USER=limix GITHUB
_PROJECT=bgen bash
[0/7] Library(bgen==3.0.3)
[1/7] Downloading... done.
[2/7] Extracting... done.
[3/7] Configuring... done.
[4/7] Compiling... FAILED.
[_/7] Log output:

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   117  100   117    0     0     20      0  0:00:05  0:00:05 --:--:--    27
100 5398k    0 5398k    0     0   423k      0 --:--:--  0:00:12 --:--:-- 1238k
-------------------------------------------------------------------------------
Hello there. This is the bgen (3.0.3) project. We wish you an easy ride.
If by any chance you find in trouble, please, do not hesitate in contacting
us at <https://github.com/limix/bgen/issues/new>.
-------------------------------------------------------------------------------
-- The C compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
-- Found ZSTD: /usr/lib/x86_64-linux-gnu/libzstd.so
-- Found ATHR: /usr/local/lib/libathr.so
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/tmp.19yjgzVBvDbgen/bgen-3.0.3/build
Scanning dependencies of target bgen_static
[  1%] Building C object CMakeFiles/bgen_static.dir/src/depr/buffer.c.o
In file included from /tmp/tmp.19yjgzVBvDbgen/bgen-3.0.3/src/depr/buffer.c:2:0:
/usr/local/include/athr.h:20:10: fatal error: athr_export.h: No such file or directory
 #include "athr_export.h"
          ^~~~~~~~~~~~~~~
compilation terminated.
CMakeFiles/bgen_static.dir/build.make:62: recipe for target 'CMakeFiles/bgen_static.dir/src/depr/buffer.c.o' failed
make[2]: *** [CMakeFiles/bgen_static.dir/src/depr/buffer.c.o] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/bgen_static.dir/all' failed
make[1]: *** [CMakeFiles/bgen_static.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2

Log file path: /tmp/tmp.iB1yutn3MHbgen.log

I then tried building the 'almost there' project first. That project worked, but did not fix the missing header when building bgen.

Thanks,
Carl

Make it requires elapsed library

find_package(elapsed REQUIRED)
target_link_libraries(bgen PUBLIC ELAPSED::elapsed)

Also check e-mail from Mikhail Kovtun to more details.

Option to write libraries in /usr/lib64

Could you add an option in CMakeLists.txt to allow change of path for libraries?

On Windows Git Bash: athr.lib is "Program Files (x86)" not "Program Files" so Bgen build fails

On Windows, I got Git Bash re-installed and got cmake, zstd, zlib, and athr installed.
athr was installed with
curl -fsSL https://git.io/JerYI | GITHUB_USER=horta GITHUB_PROJECT=almosthere bash
But athr went to "C:\Program Files (x86)\athr" instead of "C:\Program Files\athr", so
curl -fsSL https://git.io/JerYI | GITHUB_USER=limix GITHUB_PROJECT=bgen bash failed.

A work around was to copy the athr directory to "C:\Program Files\athr"

Finish I/O for BGEN file format.

Do bgen sample file determines order of the samples?

Does .bgen "sample" file determine the order of samples in the calls and all of the other genotype data sets? (similar to plink .fam file?)

There is a ncombs=3 in the code

Fix this eventually...

Magic number?

Hello there!
I used this library in my code for reading bgen files.
But then I was given an error for magic number mismatching. So I was wondering how was the magic number "1852139362" generated and why my bgen file not recognized. Many thanks!

Citation?

Is there a preferred citation for referring to this library in published work?

Windows 32 and 64 bits release with VC9 support

This is in order to support Anaconda and Miniconda distributions of Python 2.7 on Windows. @fpcasale