LibStatGen Download

Download

Click the link to download the tar of the statgen library and tools: StatGen.0.1.4.tgz‎ - Released 1/21/2011

If you use this software, please e-mail me, Mary Kate Trost, at mktrost@umich.edu

This version is recommended for Unix users with access to the GNU C++ compiler.

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

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)

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

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.