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LibStatGen Download (view source)

Revision as of 00:04, 13 November 2017

6,814 bytes added ,  00:04, 13 November 2017
→‎Official Releases
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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.1.0.6.tgz‎|LibStatGen.1.0.6.tgz‎]] - Released 11/14/2012
     −
'''LibStatGen.1.0.6 Release Notes'''
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'''LibStatGen.1.0.14 Release Notes'''
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* Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq
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*Version 1.0.14 - Released 7/8/2015
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** Updates:
+
** https://github.com/statgen/libStatGen/archive/v1.0.14.tar.gz
−
*** Fix a bug in the make install command
+
** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
 +
*** General Updates:
 +
**** Compiling Updates:
 +
***** PedigreeLoader.cpp - fix bool vs int definition
 +
***** InputFile - add 'const' to isOpen and ifeof methods. Also add comments about usage of 'operator >>'
 +
*** Bam/Tabix Updates:
 +
**** 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
 +
*** BAM Updates:
 +
**** SamFilter
 +
***** Update to clear MapQ and N/A flags when marking as unmapped
 +
***** Fix bug in clipping logic that didn't properly adjust the start position if the read was already clipped
 +
*** VCF Updates:
 +
**** Add missing include for c++11
 +
 
 +
 
 +
'''LibStatGen.1.0.13 Release Notes'''
 +
*Version 1.0.13 - Released 2/20/2015
 +
** https://github.com/statgen/libStatGen/archive/v1.0.13.tar.gz
 +
** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
 +
*** General Updates:
 +
**** Added knetfile support to InputFile (only for bgzf files if KNET_ON=1 is set on compile line
 +
**** GzipHeader - fix signed/unsigned comparison compile issue
 +
**** Upgrade bgzf (also allow append mode)
 +
*** Makefiles Updates:
 +
**** Update dependencies to fix/improve some compiling issues
 +
*** PhoneHome Updates:
 +
**** Allow PhoneHome to be a legacy parameter
 +
**** Update new version available message to stand out more
 +
**** Fix bugs in checks for new version since it wasn't finding it.
 +
*** BAM Updates:
 +
**** SamReferenceInfo operator== - fix to not check hash, since hash could be different for same info
 +
**** Pileup - improve error message for buffer overrun
 +
*** VCF Updates:
 +
**** Add option to update GT field
 +
**** Add subset samples parameter to ReadRecord
 +
**** Improve handling of adding CO header
    
''' Older Releases'''
 
''' Older Releases'''
 +
*[[Media:LibStatGen.1.0.12.tgz‎|LibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
 +
** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
 +
*** General Updates:
 +
**** Improve Makefiles for adding additional libraries/creating external libraries
 +
**** Cleanup compiling for mingw
 +
**** Cleanup Copyrights
 +
*** BAM Updates:
 +
**** Update rmTags & getTagsString to accept ',' delimiter rather than just ';'
 +
*[[Media:LibStatGen.1.0.11.tgz‎|LibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014
 +
** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
 +
*** General Updates:
 +
**** Cleanup compile warnings - should improve compatibility with Windows, RedHat, and older and newer compilers
 +
**** StringBasics: Improve off-by-one overflow handling (from github user wavexx)
 +
*** BAM Updates:
 +
**** Fix it to properly handle 'B' & 'f' tags
 +
**** Fix handling of duplicate tags
 +
*** PhoneHome Updates:
 +
**** Add parameters names (not values) to PhoneHome URL
 +
*** VCF Updates:
 +
**** Move allele count logic from VcfFileReader into VcfRecord.
 +
*[[Media:LibStatGen.1.0.10.tar.gz‎|LibStatGen.1.0.10.tar.gz‎]] - Released 1/2/2014
 +
** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
 +
*** Updates:
 +
**** Add PhoneHome/version checking logic
 +
***General Updates:
 +
**** fix use of strncpy to fix compile problem for some users
 +
**** Fix compile problem on gcc 4.8.1 by adding -Wno-strict-overflow in general/Makefile after -Werror
 +
**** Reduce the default IFILE read buffer size from 1MB to 64KB.
 +
**** Fix ifclose to take a IFILE reference so it can make the pointer 0 after closing
 +
**** StringBasics::AsInteger now returns false if the string is empty.
 +
**** GzipFileType - update to accept -.gz as stdin/stdout
 +
**** Remove unnecssary line from Parameters Status call
 +
**** Fix memory leak on Tabix destructor
 +
*** Vcf Updates:
 +
**** VCF - add class/methods to discard records based on ID
 +
*** Bam Updates:
 +
**** SamFlag - add isSecondary check
 +
**** 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
 +
**** SamRecord: Add warnings about Duplicate Tags being overwritten
 +
**** 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)
 +
*** Glf Updates:
 +
**** GlfFile cleanup bugs/handle missind endMarkers & update "get" methods to be const
 +
 +
*[[Media:LibStatGen.1.0.9.tgz‎|LibStatGen.1.0.9.tgz‎]] - Released 7/7/2013
 +
** Contains classes for general processing (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
 +
 +
 +
*[[Media:LibStatGen.1.0.8.tgz‎|LibStatGen.1.0.8.tgz‎]] - Released 1/29/2013
 +
** Contains classes for general processing (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.
 +
 +
*[[Media:LibStatGen.1.0.7.tgz‎|LibStatGen.1.0.7.tgz‎]] - Released 1/29/2013
 +
** Contains classes for general processing (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
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**** Update SamCoordOutput to add flushAll method
 +
 +
* [[Media:LibStatGen.1.0.6.tgz‎|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
 +
 
* [[Media:LibStatGen.1.0.5.tgz‎|LibStatGen.1.0.5.tgz‎]] - Released 10/24/2012
 
* [[Media:LibStatGen.1.0.5.tgz‎|LibStatGen.1.0.5.tgz‎]] - Released 10/24/2012
−
** Contains classes for general processiong (string, reference file, parameters), bam, glf, and fastq
+
** Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
 
*** Updates:
 
*** Updates:
 
**** Cleanup compile warnings
 
**** Cleanup compile warnings
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**** Update to output average qualities
 
**** Update to output average qualities
 
*[[Media:LibStatGen.1.0.2.tgz‎|LibStatGen.1.0.2.tgz‎]] - Released 05/16/2012
 
*[[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
+
** Contains classes for general processing (string, reference file, parameters), bam, glf, and fastq
 
** Additions:
 
** Additions:
 
*** Add reverseComplement method to BaseUtilities.h
 
*** 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 processing (string, reference file, parameters), bam, glf, and fastq
 
** BAM Additions:
 
** BAM Additions:
 
*** Ability to use require/exclude flags when reading
 
*** Ability to use require/exclude flags when reading
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/5963...14941"

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