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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>.
'''LibStatGen.1.0.10 Release Notes'''
'''LibStatGen.1.0.11 Release Notes'''
* Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
*[[Media:LibStatGen.1.0.11.tar.gz|LibStatGen.1.0.11.tar.gz]] - Released 2/28/2014
** Updates:
** Contains classes for general processing (string, reference file, parameters), bam, glf, fastq, and vcf
*** General Updates:
**General Updates:
**** Cleanup compile warnings - should improve compatibility with Windows, RedHat, and older and newer compilers
*** fix use of strncpy to fix compile problem for some users
**** StringBasics: Improve off-by-one overflow handling (from github user wavexx)
*** Fix compile problem on gcc 4.8.1 by adding -Wno-strict-overflow in general/Makefile after -Werror
*** BAM Updates:
*** Reduce the default IFILE read buffer size from 1MB to 64KB.
**** Fix it to properly handle 'B' & 'f' tags
**** Fix handling of duplicate tags
*** StringBasics::AsInteger now returns false if the string is empty.
*** PhoneHome Updates:
**** Add parameters names (not values) to PhoneHome URL
*** VCF Updates:
*** Fix memory leak on Tabix destructor
**** Move allele count logic from VcfFileReader into VcfRecord.
*** VCF - add class/methods to discard records based on ID
*** 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
''' Older Releases'''
''' Older Releases'''
*[[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
