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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>. |
| | | | |
| − | <span style="color:green;">'''Official Release coming soon (for now use the [[C++ Library: libStatGen#Using Git To Track the Current Development Version|development version]]).'''</span>
| + | [[Media:LibStatGen.1.0.0.tgz|LibStatGen.1.0.0.tgz]] - Released 10/10/2011 |
| | | | |
| − | = Deprecated <code>statgen</code> Repository Releases =
| + | '''LibStatGen.1.0.0 Release Notes''' |
| − | === Current Official Release ===
| + | * Initial release of libStatGen. It started from the library found in the deprecated StatGen repository. |
| − | ==== StatGen.0.1.4 ====
| + | * Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq |
| − | [[Media:StatGen.0.1.4.tgz|StatGen.0.1.4.tgz]] - Released 1/21/2011
| |
| − | | |
| − | ===== StatGen.0.1.4 Release Notes =====
| |
| − | * Added the following programs:
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| − | ** glfMerge
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| − | ** glfMultiples
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| − | * Merged latest set of core library code into lib/general
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| − | | |
| − | ===== Problems in the StatGen.0.1.4 Release =====
| |
| − | Let me know if you experience any of these problems as we may already have a fix you can use:
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| − | | |
| − | * 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
| |
| − | <pre>
| |
| − | test : all
| |
| − | if test -d $(TEST_DIR); \
| |
| − | then \
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| − | $(MAKE) $(PARALLEL_MAKE) -C $(TEST_DIR) OPTFLAG="$(OPTFLAG)" --no-print-directory $@; \
| |
| − | fi
| |
| − | | |
| − | </pre>
| |
| − | * 3/3/11 - With older versions of gcc, Line 17 of statgen/lib/general/Makefile checks if the version is > 4.1.0 to determine whether or not to use the compile option -Wno-unused-result. However, it is known that version 4.1.2 does not support that option either. If you run into this problem, you can update to 4.2.0 or some higher number if that still does not support it
| |
| − | ** Solution: Update stagen/lib/general/Makefile line 17 to the following:
| |
| − | <pre>
| |
| − | WARNINGS+=$(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-unused-result" ; fi)
| |
| − | </pre>
| |
| − | * 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:
| |
| − | <pre>
| |
| − | newPercent = (int) (1.0 * fastaIndex / fastaDataSize) * 100;
| |
| − | </pre>
| |
| − | * 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:
| |
| − | <pre>
| |
| − | //#include <omp.h>
| |
| − | </pre>
| |
| − | | |
| − | | |
| − | | |
| − | === Previous Official Releases ===
| |
| − | | |
| − | ==== StatGen.0.1.3 ====
| |
| − | [[Media:StatGen.0.1.3.tgz|StatGen.0.1.3.tgz]] - Released 1/19/2011
| |
| − | ===== StatGen.0.1.3 Release Notes =====
| |
| − | * 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 ====
| |
| − | [[Media:StatGen.0.1.2.tgz|StatGen.0.1.2.tgz]] - Released 11/17/2010
| |
| − | ===== StatGen.0.1.2 Release Notes =====
| |
| − | * 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 ====
| |
| − | [[Media:StatGen.0.1.1.tgz|StatGen.0.1.1.tgz]] - Released 11/09/2010
| |
| − | ===== StatGen.0.1.1 Release Notes =====
| |
| − | *Added QPLOT to the release
| |
| − | * Made lib/general/StringBasics.h method IsEmpty const
| |
| − | * Removed an unimplemented method from GlfRecord.h
| |
| − | | |
| − | ==== StatGen.0.1.0 ====
| |
| − | [[Media:StatGen.0.1.0.tgz|StatGen.0.1.0.tgz]] - Released 11/02/2010
| |
| − | ===== StatGen.0.1.0 Release Notes =====
| |
| − | * Original version.
| |
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.1.0.0.tgz - Released 10/10/2011
LibStatGen.1.0.0 Release Notes
- Initial release of libStatGen. It started from the library found in the deprecated StatGen repository.
- Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq
