StatgenTools

statgenTools Overview

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 bin directory.

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 libStatGen will 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:

git clone https://github.com/statgen/statgenTools.git

or

git clone git://github.com/statgen/statgenTools.git

Either of these commands create a directory called statgenTools in the current directory.

Then just 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):

1. cd pathToYourCopy/statgenTools
2. make clean
3. git pull
4. make all

Git Refresher

If you decide to use git, but need a refresher, see How To Use Git or Notes on how to use git (if you have access)

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:

1. Latest Code (master branch)

   via Website

   1. Goto: https://github.com/statgen/statgenTools
   2. Click on the Download ZIP button on the right side panel.

   via Command Line

   wget https://github.com/statgen/statgenTools/archive/master.tar.gz

   or

   wget https://github.com/statgen/statgenTools/archive/master.zip

2. Specific Release (via a tag)

   via Website

   1. Goto: https://github.com/statgen/statgenTools/releases to see the available releases
   2. Click zip or tar.gz for the desired version.

   via Command Line

   wget https://github.com/statgen/statgenTools/archive/<tagName>.tar.gz

   or

   wget https://github.com/statgen/statgenTools/archive/<tagName>.zip

After downloading the file, uncompress (unzip/untar) it. The directory created will be named statgenTools-<name of version you downloaded>.

Building

After obtaining the statgenTools repository (either by download or from github), compile the code using:

make all  

Object (.o) files are compiled into the obj directory with a subdirectory debug and 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 statgenTools/bin/profile/ directory.

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 test subdirectory).

To see all make options, type make help.

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 -Werror.

Releases

Release downloads are Coming Soon.

Programs/Tools

The statgenTools repository contains the following tools:

• createUMref - Create the University of Michigan formatted reference used by many of our tools.

These executables are built using C++ Library: libStatGen.

Just running the executable with no options will print the Usage information for the executable.

createUMref

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