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LibStatGen Download (view source)

Revision as of 00:04, 13 November 2017

7,293 bytes added ,  00:04, 13 November 2017
→‎Official Releases
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[[Category:Software]]
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= General libStatGen Information =
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[[Category:C++]]
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See [[C++ Library: libStatGen]].
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[[Category:libStatGen]]
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== Download ==
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= Latest Development Versions =
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Click the link to download the tar of the statgen library and tools: [[Media:StatGen.0.1.4.tgz‎|StatGen.0.1.4.tgz‎]] - Released 1/21/2011
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For information about obtaining the latest Development Versions, see [[C++ Library: libStatGen#Where to Find It|Where to Find libStatGen]]
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'''If you use this software, please e-mail me, Mary Kate Trost, at mktrost@umich.edu'''
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= Official Releases =
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If you prefer to run the last official release rather than the latest development version, you can download that here.
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This version is recommended for Unix users with access to the GNU C++ compiler.
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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>.  
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To install, unpack the downloaded file (tar xvf), cd into the statgen directory and type make.
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=== Dependencies ===
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'''LibStatGen.1.0.14 Release Notes'''
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* This software requires the following to be installed:
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*Version 1.0.14 - Released 7/8/2015
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** g++
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** https://github.com/statgen/libStatGen/archive/v1.0.14.tar.gz
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** development version of zlib (zlib1g-dev on ubuntu)
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** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
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** openssl and md5 (libssl-dev on ubuntu)
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*** General Updates:
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** curses (libcurses-perl on ubuntu)
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**** Compiling Updates:
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***** PedigreeLoader.cpp - fix bool vs int definition
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***** InputFile - add 'const' to isOpen and ifeof methods. Also add comments about usage of 'operator >>'
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*** Bam/Tabix Updates:
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**** Update how the index is stored in memory to not preallocate the maximum number of bins for each reference as this could use a lot of memory if there are a lot of references
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*** BAM Updates:
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**** SamFilter
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***** Update to clear MapQ and N/A flags when marking as unmapped
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***** Fix bug in clipping logic that didn't properly adjust the start position if the read was already clipped
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*** VCF Updates:
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**** Add missing include for c++11
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=== Notes ===
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* '''Current Release Notes''' (1/21/2011)
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** 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 Current Release ===
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'''LibStatGen.1.0.13 Release Notes'''
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Let me know if you experience any of these problems as we may already have a fix you can use:
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*Version 1.0.13 - Released 2/20/2015
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** https://github.com/statgen/libStatGen/archive/v1.0.13.tar.gz
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** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
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*** General Updates:
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**** Added knetfile support to InputFile (only for bgzf files if KNET_ON=1 is set on compile line
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**** GzipHeader - fix signed/unsigned comparison compile issue
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**** Upgrade bgzf (also allow append mode)
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*** Makefiles Updates:
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**** Update dependencies to fix/improve some compiling issues
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*** PhoneHome Updates:
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**** Allow PhoneHome to be a legacy parameter
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**** Update new version available message to stand out more
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**** Fix bugs in checks for new version since it wasn't finding it.
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*** BAM Updates:
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**** SamReferenceInfo operator== - fix to not check hash, since hash could be different for same info
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**** Pileup - improve error message for buffer overrun
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*** VCF Updates:
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**** Add option to update GT field
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**** Add subset samples parameter to ReadRecord
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**** Improve handling of adding CO header
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* 1/24/11 - glfMultiples does not have a 'test' target, so 'make test' fails.
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''' Older Releases'''
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** Solution: Add the following at line 89 of statgen/src/glfMultiples/Makefile
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*[[Media:LibStatGen.1.0.12.tgz‎|LibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
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<pre>
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** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
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test : all
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*** General Updates:
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if test -d $(TEST_DIR); \
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**** Improve Makefiles for adding additional libraries/creating external libraries
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        then \
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**** Cleanup compiling for mingw
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        $(MAKE) $(PARALLEL_MAKE) -C $(TEST_DIR) OPTFLAG="$(OPTFLAG)" --no-print-directory $@; \
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**** Cleanup Copyrights
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        fi
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*** BAM Updates:
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**** Update rmTags & getTagsString to accept ',' delimiter rather than just ';'
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*[[Media:LibStatGen.1.0.11.tgz‎|LibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014
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** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
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*** General Updates:
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**** Cleanup compile warnings - should improve compatibility with Windows, RedHat, and older and newer compilers
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**** StringBasics: Improve off-by-one overflow handling (from github user wavexx)
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*** BAM Updates:
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**** Fix it to properly handle 'B' & 'f' tags
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**** Fix handling of duplicate tags
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*** PhoneHome Updates:
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**** Add parameters names (not values) to PhoneHome URL
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*** VCF Updates:
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**** Move allele count logic from VcfFileReader into VcfRecord.
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*[[Media:LibStatGen.1.0.10.tar.gz‎|LibStatGen.1.0.10.tar.gz‎]] - Released 1/2/2014
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** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
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*** Updates:
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**** Add PhoneHome/version checking logic
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***General Updates:
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**** fix use of strncpy to fix compile problem for some users
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**** Fix compile problem on gcc 4.8.1 by adding -Wno-strict-overflow in general/Makefile after -Werror
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**** Reduce the default IFILE read buffer size from 1MB to 64KB.
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**** Fix ifclose to take a IFILE reference so it can make the pointer 0 after closing
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**** StringBasics::AsInteger now returns false if the string is empty.
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**** GzipFileType - update to accept -.gz as stdin/stdout
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**** Remove unnecssary line from Parameters Status call
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**** Fix memory leak on Tabix destructor
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*** Vcf Updates:
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**** VCF - add class/methods to discard records based on ID
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*** Bam Updates:
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**** SamFlag - add isSecondary check
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**** Fix SamFile so it only allows '-', '-.sam', '-.bam', or '-.ubam' to indicate reading from stdin rather than anything that starts with '-' in order to protect it from misinterpreting another parameter as the stdin filename
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**** SamRecord: Add warnings about Duplicate Tags being overwritten
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**** SamFile - improve sort order validation error messages and compare using both String::Compare and strcmp to handle various sort mechanisms since neither matches samtools exactly (if either is successful, the sort order is OK)
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*** Glf Updates:
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**** GlfFile cleanup bugs/handle missind endMarkers & update "get" methods to be const
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</pre>
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*[[Media:LibStatGen.1.0.9.tgz‎|LibStatGen.1.0.9.tgz‎]] - Released 7/7/2013
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** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
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*** Updates:
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**** Update Makefile processing to check for a Makefile in the test directory before recursively calling make in there
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**** Replace CFLAGS wtih COMPFLAGS
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**** Update the Windows WIN32 if statements
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***General Updates:
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**** Add boundary check to StringBasics memory
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**** Added support for new CIGAR characters (X & =)
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**** Update bug in PedigreeLoader to specify WHITESPACE
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**** add accessors for getting tabix information
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*** Vcf Updates:
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**** add ability to drop trailing missing Genotype fields
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**** check that the tabix index is for VCF file type
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**** Fix broken dependency
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*** Bam Updates:
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**** SamHeaderRecord: add accessor to get the value for the key
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**** update some classes to have virtual destructors
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=== Troubleshooting ===
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If you are having trouble compiling, check [[StatGen Troubleshooting]] for help.  If that does not solve your problem, email me for support.
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=== Previous Versions ===
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*[[Media:LibStatGen.1.0.8.tgz‎|LibStatGen.1.0.8.tgz‎]] - Released 1/29/2013
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* [[Media:StatGen.0.1.3.tgz‎|StatGen.0.1.3.tgz‎]] - Released 1/19/2011
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** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
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** Added the following programs:
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*** Updates:
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*** mgpileup
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**** Added VCF file handling (merged the vcf branch to master)
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*** thunderVCF
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**** Add support for reading Tabix files
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*** vcfCooker
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**** Add ReusableVector class that holds vectors that will remove only the last or be reset & reused without clearing memory.
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*** verifyBamID
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** BAM
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*[[Media:LibStatGen.1.0.7.tgz‎|LibStatGen.1.0.7.tgz‎]] - Released 1/29/2013
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*** Fixed bug in SamQuerySeqWithRefIter
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** Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
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*** Add handling of the reference to the SAM Library to allow the conversion of SAM Record Sequence to/from using '=' or just bases.
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*** Updates:
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**** Add the conversion to/from '=' in the sequence to the bam Convert program.
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**** Add operator== to StringIntHash
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*** Add the ability to read the header when opening a BAM/SAM file.
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**** Cleanup compiling for files that are just headers with no .cpp
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*** Update SetReadSection to reset the data for validating sorting since it can jump around in the file.
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**** Update Makefile TOOLOBJ to handle fortran
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** GLF
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**** ReferenceSequence.h fix compile problem on upgraded system
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*** Fixed bug that incorrectly wrote GLF Records of type 2
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**** Add Makefile.extlib for compiling libraries that use libStatGen
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*** 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. 
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*** BAM Updates:
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** FastQ
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**** Update to allow copying SamHeaderRecords and automatically update the SQ ReferenceInfo
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*** Add option to not check for uniqueness of the sequence identifier
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**** Update SamFileHeader::getReferenceInfo() to return a SamReferenceInfo reference rather than ptr
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** OTHER
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**** Update SamRecord::getStringTag to return a const string pointer instead of just a string pointer
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*** removed zlib from being included in the repository.
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**** Update SamCoordOutput to add flushAll method
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* [[Media:StatGen.0.1.2.tgz|StatGen.0.1.2.tgz]] - Released 11/09/2010
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** FASTQ
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* [[Media:LibStatGen.1.0.6.tgz‎|LibStatGen.1.0.6.tgz‎]] - Released 11/14/2012
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*** Add option to disable the unique sequence identifier check since that uses a lot of memory.
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** Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
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** GLF
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*** Updates:
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*** Automatically write the End Maker record when writing GLF files.
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**** Fix a bug in the make install command
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*** Add capability of consuming records to get to the next reference section.
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*** Fixed bug in writing GLF records of type 2.
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* [[Media:LibStatGen.1.0.5.tgz‎|LibStatGen.1.0.5.tgz‎]] - Released 10/24/2012
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** Other
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** Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
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*** Remove ZLIB from being contained within the repository (having zlib in the repository may have caused some compile issues in the previous version).
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*** Updates:
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* [[Media:StatGen.0.1.1.tgz|StatGen.0.1.1.tgz]] - Released 11/09/2010
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**** Cleanup compile warnings
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**Added QPLOT to the release
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**** Support compiling without ZLIB (use: make ZLIB_AVAIL=0)
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** Made lib/general/StringBasics.h method IsEmpty const
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*** BAM Updates:
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** Removed an unimplemented method from GlfRecord.h
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**** Update to add error messages about failing to add a header
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* [[Media:StatGen.0.1.0.tgz|StatGen.0.1.0.tgz]] - Released 11/02/2010
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**** Handle a vtype of 'B' in the TAG field (treats it like a string)
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** Original version.
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* LibStatGen.1.0.4.tgz‎ - Released skipped
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*[[Media:LibStatGen.1.0.3.tgz‎|LibStatGen.1.0.3.tgz‎]] - Released 09/19/2012
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** Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
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*** Additions:
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**** Fix Makefile COMPILE_ANY_CHANGE logic to actually work
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**** Fix compile problems on macs
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***** Add #include <cstddef> to GzipFileType.h & #include <unistd.h> to MemoryMapArray.h
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*** General Additions:
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**** Update DBSNP processing in GenomeSequence to also accept gzipped files
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**** Add support of fasta files in GenomeSequence
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**** Update GenomeSequence constructor/open to create the umfa version if it doesn't already exist
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**** Update StringAlias to add getAliases
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**** Update StringHash to have an option to do case sensitive (instead of always case-insensitive)
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**** Make library building PHONY so it is always checked for updates and only updated if objects are newer
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*** BAM Additions:
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**** Update BamIndex hex constant to use ULL
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**** Cleanup handling of header errors
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**** Update SamFileHeader to use case sensitive hashes
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**** Make repeated header line keys a warning, not an error
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*** FASTQ Additions:
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**** Update to output average qualities
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*[[Media:LibStatGen.1.0.2.tgz‎|LibStatGen.1.0.2.tgz‎]] - Released 05/16/2012
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** Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
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** Additions:
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*** Add reverseComplement method to BaseUtilities.h
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*[[Media:LibStatGen.1.0.1.tgz‎|LibStatGen.1.0.1.tgz‎]] - Released 05/04/2012
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** Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
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** BAM Additions:
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*** Ability to use require/exclude flags when reading
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*** CigarHelper for soft clipping
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*** Fixed bug in BamIndex that wasn't closing the file
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*** Additional cleanup/updates, see https://github.com/statgen/libStatGen/commits/master/bam for all changes between 10/10/2011 and 05/04/2012.
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** General Additions:
 +
*** Modifications to improve file handling/string processing
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*** Fixed some compile warnings
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*** Update Parameters class to always print warnings about unknown parameters to stderr
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*** Update PedigreePerson to create/delete the strings object
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*** Cleanup GenomeSequence to remove code that is also in BaseAsciiMap
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** Samtools Modifications:
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*** Do not use knetfile and fix compile warning
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*[[Media:LibStatGen.1.0.0.tgz‎|LibStatGen.1.0.0.tgz‎]] - Released 10/10/2011
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** 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.
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/2999...14941"

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