3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Official Releases
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>.
'''LibStatGen.1.0.10 Release Notes'''
'''LibStatGen.1.0.14 Release Notes'''
* Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
*Version 1.0.14 - Released 7/8/2015
** Updates:
** https://github.com/statgen/libStatGen/archive/v1.0.14.tar.gz
*** Add PhoneHome/version checking logic
** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
**General Updates:
*** General Updates:
*** fix use of strncpy to fix compile problem for some users
**** Compiling Updates:
*** Fix compile problem on gcc 4.8.1 by adding -Wno-strict-overflow in general/Makefile after -Werror
***** PedigreeLoader.cpp - fix bool vs int definition
*** Reduce the default IFILE read buffer size from 1MB to 64KB.
***** InputFile - add 'const' to isOpen and ifeof methods. Also add comments about usage of 'operator >>'
*** Fix ifclose to take a IFILE reference so it can make the pointer 0 after closing
*** Bam/Tabix Updates:
*** StringBasics::AsInteger now returns false if the string is empty.
**** 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
*** GzipFileType - update to accept -.gz as stdin/stdout
*** BAM Updates:
*** Remove unnecssary line from Parameters Status call
**** SamFilter
*** Fix memory leak on Tabix destructor
***** 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 - add class/methods to discard records based on ID
*** VCF Updates:
** Bam Updates:
**** Add missing include for c++11
*** 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
'''LibStatGen.1.0.13 Release Notes'''
*** 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)
*Version 1.0.13 - Released 2/20/2015
** Glf Updates:
** https://github.com/statgen/libStatGen/archive/v1.0.13.tar.gz
*** GlfFile cleanup bugs/handle missind endMarkers & update "get" methods to be const
** 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
*[[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
** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
