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 (coming soon) and via github.

On github, you can both browse and download the latest version of the repository as well as explore the history of changes.

You can access the latest version with or without git.

If you download from github or use git to keep up to date, you also need to download our library: libStatGen.

The releases will be available both with and without libStatGen included. If you download the verison without libStatGen included, you will also need to download libStatGen separately. (It will be available without libStatGen in case you already have a downloaded version of libStatGen that you want to use.

Releases

Release downloads are Coming Soon.

Using github

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

Periodically download the latest copy from github from the "Downloads" link on the webpage: https://github.com/statgen/statgenTools/archives/master.

The downloaded tar file is named "statgen-statgenTools-someHexNumber.tar.gz". The directory created when it is untared shares the same base name. I recommend that you do not change the name of the directory. If you want one called statgenTools, create a link to this directory. The hex number in the directory name identifies the version of the repository that you downloaded and is necessary to easily troubleshoot any issues you encounter. If you must rename the directory, be sure to record the hex number that was on the download for future reference.

Building

After obtaining the statgenTools repository (either by download or from github), compile the code using make all. This creates the executable all the executables in the statgenTools/bin/ directory, the debug executables in the statgenTools/bin/debug/ directory, and the profiling executables in the statgenTools/bin/profile/ directory.

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