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[[Category:libStatGen]]
[[Category:libStatGen]]
= Dependencies =
* This software requires the following to be installed:
* This software requires the following to be installed:
** g++
** g++
** curses (libcurses-perl on ubuntu)
** curses (libcurses-perl on ubuntu)
== Download ==
= Troubleshooting =
If you are having trouble compiling any of the versions, check [[StatGen Troubleshooting]] for help. If that does not solve your problem, email me for support.
= Download =
'''If you use this software, please e-mail me, Mary Kate Trost, at mktrost@umich.edu'''
'''If you use this software, please e-mail me, Mary Kate Trost, at mktrost@umich.edu'''
Currently the repository is recommended for Unix/Linux users with access to the GNU C++ compiler.
Currently the repository is recommended for Unix/Linux users with access to the GNU C++ compiler.
== github : Latest Development Version ==
The development version of the statgen repository is found on github and can be used either with or without git: https://github.com/statgen/statgen
The development version of the statgen repository is found on github and can be used either with or without git: https://github.com/statgen/statgen
On the github website, you can browse and/or download the code.
On the github website, you can browse and/or download the code.
=== Using git ===
Just a couple of simple steps to obtain the repository:
Just a couple of simple steps to obtain the repository:
# cd <directory where you want the repository located>
# cd <directory where you want the repository located>
# Recompile from the top level (use a make clean first)
# Recompile from the top level (use a make clean first)
=== Without git ===
Directions for downloading the repository from github without using git are found in: [[Media:GithubWithoutGit.pdf | GithubWithoutGit.pdf]]
Directions for downloading the repository from github without using git are found in: [[Media:GithubWithoutGit.pdf | GithubWithoutGit.pdf]]
Periodically you should download the latest version of the repository following the download instructions again.
Periodically you should download the latest version of the repository following the download instructions again.
== Official Releases ==
If you prefer to run the last official release rather than the latest development version, you can download that here.
If you prefer to run the last official release rather than the latest development version, you can download that here.
To install an official release, unpack the downloaded file (tar xvf), cd into the statgen directory and type make.
=== Current Official Release ===
==== StatGen.0.1.4 ====
[[Media:StatGen.0.1.4.tgz|StatGen.0.1.4.tgz]] - Released 1/21/2011]
===== StatGen.0.1.4 Release Notes =====
* Added the following programs:
** glfMerge
** glfMultiples
* Merged latest set of core library code into lib/general
=== Notes ===
===== Problems in the StatGen.0.1.4 Release =====
=== Problems in Current Release ===
Let me know if you experience any of these problems as we may already have a fix you can use:
Let me know if you experience any of these problems as we may already have a fix you can use:
=== Troubleshooting ===
=== Previous Official Releases ===
==== StatGen.0.1.3 ====
[[Media:StatGen.0.1.3.tgz|StatGen.0.1.3.tgz]] - Released 1/19/2011
===== StatGen.0.1.3 Release Notes =====
* Added the following programs:
** mgpileup
** thunderVCF
** vcfCooker
** verifyBamID
* BAM
** Fixed bug in SamQuerySeqWithRefIter
** Add handling of the reference to the SAM Library to allow the conversion of SAM Record Sequence to/from using '=' or just bases.
*** Add the conversion to/from '=' in the sequence to the bam Convert program.
** Add the ability to read the header when opening a BAM/SAM file.
** Update SetReadSection to reset the data for validating sorting since it can jump around in the file.
* GLF
** Fixed bug that incorrectly wrote GLF Records of type 2
** Add capability to consume remaining records when getNextRefSection is called. Also when writing automatically write the End Marker if it was not already written when a new RefSection is written or when the file is closed.
* FastQ
** Add option to not check for uniqueness of the sequence identifier
* OTHER
** removed zlib from being included in the repository.
==== StatGen.0.1.2 ====
[[Media:StatGen.0.1.2.tgz|StatGen.0.1.2.tgz]] - Released 11/17/2010
===== StatGen.0.1.2 Release Notes =====
* FASTQ
** Add option to disable the unique sequence identifier check since that uses a lot of memory.
* GLF
** Automatically write the End Maker record when writing GLF files.
** Add capability of consuming records to get to the next reference section.
** Fixed bug in writing GLF records of type 2.
* Other
** Remove ZLIB from being contained within the repository (having zlib in the repository may have caused some compile issues in the previous version).
==== StatGen.0.1.1 ====
[[Media:StatGen.0.1.1.tgz|StatGen.0.1.1.tgz]] - Released 11/09/2010
===== StatGen.0.1.1 Release Notes =====
*Added QPLOT to the release
* Made lib/general/StringBasics.h method IsEmpty const
* Removed an unimplemented method from GlfRecord.h
=== Previous Versions ===
==== StatGen.0.1.0 ====
[[Media:StatGen.0.1.0.tgz|StatGen.0.1.0.tgz]] - Released 11/02/2010
===== StatGen.0.1.0 Release Notes =====
* Original version.
