Difference between revisions of "LibStatGen Download"
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* '''Current Release Notes''' (1/19/2011) | * '''Current Release Notes''' (1/19/2011) | ||
| − | ** | + | ** Added the following programs: |
| − | *** Add | + | *** 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 | ** GLF | ||
| − | *** | + | *** Fixed bug that incorrectly wrote GLF Records of type 2 |
| − | *** Add capability | + | *** 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. | ||
| + | |||
=== Problems in Current Release === | === Problems in Current Release === | ||
Revision as of 19:26, 19 January 2011
Download
Click the link to download the tar of the statgen library and tools: StatGen.0.1.3.tgz - Released 1/19/2011
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.
Notes
- This software requires zlib to be installed on your machines.
- This software requires openssl and md5 (libssl-dev on ubuntu)
- Current Release Notes (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.
- Added the following programs:
- 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.
- GLF
Problems in Current Release
Let me know if you experience any of these problems as we may already have a fix you can use:
- None reported yet.
Previous Versions
- 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).
- FASTQ
- 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.
