LibStatGen Download

Dependencies

• This software requires the following to be installed:
  • g++
  • development version of zlib (zlib1g-dev on ubuntu)
  • openssl and md5 (libssl-dev on ubuntu)
  • curses (libcurses-perl on ubuntu)

Download

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.

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

On the github website, you can browse and/or download the code.

Using git

Just a couple of simple steps to obtain the repository:

1. cd <directory where you want the repository located>
2. git clone https://github.com/statgen/statgen.git
   • Creates a directory called statgen in the directory where you are located.
3. cd statgen

Periodically you should bring in the latest version of the repository (advantage of using git):

1. cd <your statgen directory>
2. git pull
3. 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: GithubWithoutGit.pdf

Periodically you should download the latest version of the repository following the download instructions again.

Official Release

If you prefer to run the last official release rather than the latest development version, you can download that here.

Download the statgen library and tools: StatGen.0.1.4.tgz‎ - Released 1/21/2011

To install, unpack the downloaded file (tar xvf), cd into the statgen directory and type make.

Notes

• Current Release Notes (1/21/2011)
  • Added the following programs:
    • glfMerge
    • glfMultiples
  • Merged latest set of core library code into lib/general

Problems in Current Release

Let me know if you experience any of these problems as we may already have a fix you can use:

• 1/24/11 - glfMultiples does not have a 'test' target, so 'make test' fails.
  • Solution: Add the following at line 89 of statgen/src/glfMultiples/Makefile

test : all
	if test -d $(TEST_DIR); \
        then \
        $(MAKE) $(PARALLEL_MAKE) -C $(TEST_DIR) OPTFLAG="$(OPTFLAG)" --no-print-directory $@; \
        fi

• 3/3/11 - With older versions of gcc, Line 17 of statgen/lib/general/Makefile checks if the version is > 4.1.0 to determine whether or not to use the compile option -Wno-unused-result. However, it is known that version 4.1.2 does not support that option either. If you run into this problem, you can update to 4.2.0 or some higher number if that still does not support it
  • Solution: Update stagen/lib/general/Makefile line 17 to the following:

WARNINGS+=$(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-unused-result" ; fi)

• 3/3/11 - With some compilers, GenomeSequence.cpp has a compile error: "GenomeSequence.cpp:552: warning: converting to `int' from `double'"
  • Solution: Update statgen/lib/general/GenomeSequence.cpp line 552 to the following:

            newPercent = (int) (1.0 * fastaIndex / fastaDataSize) * 100;

• 3/7/11 - If you don't have openmp, you may get the following error: qplot/BamQC.cpp:4:17: omp.h: No such file or directory
  • Solution: Since qplot does not use Update statgen/src/qplot/qplot/BamQC.cpp line 4 to the following:

//#include <omp.h>

Troubleshooting

If you are having trouble compiling, check StatGen Troubleshooting for help. If that does not solve your problem, email me for support.

Previous Versions

• StatGen.0.1.3.tgz‎ - Released 1/19/2011
  • 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.tgz - Released 11/09/2010
  • 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.tgz - Released 11/09/2010
  • Added QPLOT to the release
  • Made lib/general/StringBasics.h method IsEmpty const
  • Removed an unimplemented method from GlfRecord.h
• StatGen.0.1.0.tgz - Released 11/02/2010
  • Original version.