Difference between revisions of "LibStatGen Download"
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To install an official release, unpack the downloaded file (tar xvf), cd into the libStatGen directory and type <code>make all</code>. | To install an official release, unpack the downloaded file (tar xvf), cd into the libStatGen directory and type <code>make all</code>. | ||
| − | [[Media:LibStatGen.1.0. | + | [[Media:LibStatGen.1.0.3.tgz|LibStatGen.1.0.3.tgz]] - Released 09/19/2012 |
| − | '''LibStatGen.1.0. | + | '''LibStatGen.1.0.3 Release Notes''' |
* Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq | * Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq | ||
| − | * Additions: | + | ** Additions: |
| − | ** Add | + | *** 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 | ||
''' Older Releases''' | ''' Older Releases''' | ||
| + | *[[Media:LibStatGen.1.0.2.tgz|LibStatGen.1.0.2.tgz]] - Released 05/16/2012 | ||
| + | ** Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq | ||
| + | ** Additions: | ||
| + | *** Add reverseComplement method to BaseUtilities.h | ||
*[[Media:LibStatGen.1.0.1.tgz|LibStatGen.1.0.1.tgz]] - Released 05/04/2012 | *[[Media:LibStatGen.1.0.1.tgz|LibStatGen.1.0.1.tgz]] - Released 05/04/2012 | ||
** Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq | ** Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq | ||
Revision as of 17:15, 19 September 2012
General libStatGen Information
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.1.0.3.tgz - Released 09/19/2012
LibStatGen.1.0.3 Release Notes
- Contains classes for general processiong (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
- Additions:
Older Releases
- LibStatGen.1.0.2.tgz - Released 05/16/2012
- Contains classes for general processiong (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 processiong (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.
