LibStatGen Download

General libStatGen Information

See C++ Library: libStatGen.

Latest Development Versions

For information about obtaining the latest Development Versions, see Where to Find libStatGen

Official Releases

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 libStatGen directory and type make all.

LibStatGen.1.0.9.tgz‎ - Released 7/7/2013

LibStatGen.1.0.9 Release Notes

• Contains classes for general processiong (string, reference file, parameters), bam, glf, fastq, and vcf
  • Updates:
    • Update Makefile processing to check for a Makefile in the test directory before recursively calling make in there
    • Replace CFLAGS wtih COMPFLAGS
    • Update the Windows WIN32 if statements
  • General Updates:
    • Add boundary check to StringBasics memory
    • Added support for new CIGAR characters (X & =)
    • Update bug in PedigreeLoader to specify WHITESPACE
    • add accessors for getting tabix information
  • Vcf Updates:
    • add ability to drop trailing missing Genotype fields
    • check that the tabix index is for VCF file type
    • Fix broken dependency
  • Bam Updates:
    • SamHeaderRecord: add accessor to get the value for the key
    • update some classes to have virtual destructors

Older Releases

• LibStatGen.1.0.8.tgz‎ - Released 1/29/2013
  • Contains classes for general processiong (string, reference file, parameters), bam, glf, fastq, and vcf
    • Updates:
      • Added VCF file handling (merged the vcf branch to master)
      • Add support for reading Tabix files
      • Add ReusableVector class that holds vectors that will remove only the last or be reset & reused without clearing memory.

• LibStatGen.1.0.7.tgz‎ - Released 1/29/2013
  • Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq
    • Updates:
      • Add operator== to StringIntHash
      • Cleanup compiling for files that are just headers with no .cpp
      • Update Makefile TOOLOBJ to handle fortran
      • ReferenceSequence.h fix compile problem on upgraded system
      • Add Makefile.extlib for compiling libraries that use libStatGen
    • BAM Updates:
      • Update to allow copying SamHeaderRecords and automatically update the SQ ReferenceInfo
      • Update SamFileHeader::getReferenceInfo() to return a SamReferenceInfo reference rather than ptr
      • Update SamRecord::getStringTag to return a const string pointer instead of just a string pointer
      • Update SamCoordOutput to add flushAll method

• LibStatGen.1.0.6.tgz‎ - Released 11/14/2012
  • Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
    • Updates:
      • Fix a bug in the make install command

• LibStatGen.1.0.5.tgz‎ - Released 10/24/2012
  • Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
    • Updates:
      • Cleanup compile warnings
      • Support compiling without ZLIB (use: make ZLIB_AVAIL=0)
    • BAM Updates:
      • Update to add error messages about failing to add a header
      • Handle a vtype of 'B' in the TAG field (treats it like a string)

• LibStatGen.1.0.4.tgz‎ - Released skipped
• LibStatGen.1.0.3.tgz‎ - Released 09/19/2012
  • Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
    • Additions:
      • Fix Makefile COMPILE_ANY_CHANGE logic to actually work
      • Fix compile problems on macs
        • Add #include <cstddef> to GzipFileType.h & #include <unistd.h> to MemoryMapArray.h
    • General Additions:
      • Update DBSNP processing in GenomeSequence to also accept gzipped files
      • Add support of fasta files in GenomeSequence
      • Update GenomeSequence constructor/open to create the umfa version if it doesn't already exist
      • Update StringAlias to add getAliases
      • Update StringHash to have an option to do case sensitive (instead of always case-insensitive)
      • Make library building PHONY so it is always checked for updates and only updated if objects are newer
    • BAM Additions:
      • Update BamIndex hex constant to use ULL
      • Cleanup handling of header errors
      • Update SamFileHeader to use case sensitive hashes
      • Make repeated header line keys a warning, not an error
    • FASTQ Additions:
      • Update to output average qualities
• LibStatGen.1.0.2.tgz‎ - Released 05/16/2012
  • Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
  • Additions:
    • Add reverseComplement method to BaseUtilities.h
• LibStatGen.1.0.1.tgz‎ - Released 05/04/2012
  • Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
  • BAM Additions:
    • Ability to use require/exclude flags when reading
    • CigarHelper for soft clipping
    • Fixed bug in BamIndex that wasn't closing the file
    • Additional cleanup/updates, see https://github.com/statgen/libStatGen/commits/master/bam for all changes between 10/10/2011 and 05/04/2012.
  • General Additions:
    • Modifications to improve file handling/string processing
    • Fixed some compile warnings
    • Update Parameters class to always print warnings about unknown parameters to stderr
    • Update PedigreePerson to create/delete the strings object
    • Cleanup GenomeSequence to remove code that is also in BaseAsciiMap
  • Samtools Modifications:
    • Do not use knetfile and fix compile warning

• LibStatGen.1.0.0.tgz‎ - Released 10/10/2011
  • Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq
  • Initial release of libStatGen. It started from the library found in the deprecated StatGen repository.