- 1 statgenTools Overview
- 2 Programs/Tools
statgenTools is a repository that contains programs that perform operations for our statistical genetic processing. Each program builds its own executable. This repository was created to group simple, small tools into one place. The executables will be put in the
Where to Find It
The statgenTools repository is available both via release downloads and via github.
On github, https://github.com/statgen/statgenTools, you can both browse and download the statgenTools source code as well as explore the history of changes.
You can obtain the source either with or without git.
The releases may be available both with and without libStatGen included.
If you do not use the release version that already contains libStatGen, you need to download the library: libStatGen.
If you try to compile statgenTools and it cannot find libStatGen, it will fail and provide instructions of what to do next:
- if libStatGen is in a different location then expected
- follow the directions to set the path to libStatGen
- if libStatGen is not downloaded and you have git
make libStatGenwill download via git and build libStatGen
- if libStatGen is not downloaded and you don't have git
- See libStatGen
Using Git To Track the Current Development Version
Clone (get your own copy)
You can create your own git clone (copy) using:
Either of these commands create a directory called
statgenTools in the current directory.
cd statgenTools and compile.
Get the latest Updates (update your copy)
To update your copy to the latest version (a major advantage of using git):
Downloading From GitHub Without Git
If you download the latest code/version, make sure you periodically update it by downloading a newer version.
From github you can download:
- Latest Code (master branch)
- via Website
- Goto: https://github.com/statgen/statgenTools
- Click on the
Download ZIPbutton on the right side panel.
- via Command Line
- via Website
- Specific Release (via a tag)
After downloading the file, uncompress (unzip/untar) it. The directory created will be named
statgenTools-<name of version you downloaded>.
After obtaining the statgenTools repository (either by download or from github), compile the code using:
Object (.o) files are compiled into the
obj directory with a subdirectory
profile for the debugging and profiling objects.
This creates the executable(s) in the
statgenTools/bin/ directory, the debug executable(s) in the
statgenTools/bin/debug/ directory, and the profiling executable(s) in the
make install installs the opt binary if you have permission.
make test compiles for opt, debug, and profile and runs the tests (found in the
To see all make options, type
If compilation fails due to warnings being treated as errors, please contact us so we can fix the warnings. As a work-around to get it to compile, you can disable the treatment of warnings as errors by editing libStatGen/general/Makefile to remove
Release downloads are Coming Soon.
statgenTools repository contains the following tools:
These executables are built using C++ Library: libStatGen.
Just running the executable with no options will print the Usage information for the executable.
Create the UM reference from the .fa file.
Usage: createUMref [--mmap] [--force] refFileName.fa --mmap : toggle whether to use memory map (default: true) --force: toggle whether to force creation even if it already exists