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[[Media:BamUtilLibStatGen.1.0.9.tgz|BamUtilLibStatGen.1.0.9.tgz]] - Released 7/7/2013
[[Media:BamUtilLibStatGen.1.0.10.tar.gz|BamUtilLibStatGen.1.0.10.tar.gz]] - Released 1/2/2014
'''BamUtilLibStatGen.1.0.9 Release Notes'''
'''BamUtilLibStatGen.1.0.10 Release Notes'''
* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]]
* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]] - see link for version updates
* Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.9]]
* Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.10]] - see link for version updates
* Update to [[BamUtil: mergeBam|mergeBam]]
* Adds PhoneHome/Version checking.
'''Older Releases'''
'''Older Releases'''
* There is no version 1.0.8. It was skipped to stya in line with libStatGen versions (libStatGen 1.0.8 added vcf support)
*[[Media:BamUtilLibStatGen.1.0.9.tgz|BamUtilLibStatGen.1.0.9.tgz]] - Released 7/7/2013
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]]
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.9]]
** Update to [[BamUtil: mergeBam|mergeBam]]
*** Update to ignore PG lines with duplicate IDs
*** Update to accept merges of matching RG lines
*** Update to log to stderr if no log/out file is specified
* There is no version 1.0.8. It was skipped to stay in line with libStatGen versions (libStatGen 1.0.8 added vcf support)
*[[Media:BamUtilLibStatGen.1.0.7.tgz|BamUtilLibStatGen.1.0.7.tgz]] - Released 1/29/2013
*[[Media:BamUtilLibStatGen.1.0.7.tgz|BamUtilLibStatGen.1.0.7.tgz]] - Released 1/29/2013
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]]
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]]
To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
* [[Media:BamUtil.1.0.9.tgz|BamUtil.1.0.9.tgz]] - Released 7/7/2013
* [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz]] - Released 1/2/2014
'''BamUtil.1.0.9 Release Notes'''
'''BamUtil.1.0.10 Release Notes'''
* Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]] (version 1.0.7 should also work)
* [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz]] - Released 1/2/2014
* Update to [[BamUtil: mergeBam|mergeBam]]
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]]
** Update to ignore PG lines with duplicate IDs
** All
** Update to accept merges of matching RG lines
*** Add PhoneHome/version checking
** Update to log to stderr if no log/out file is specified
*** Make sub-program names case independent
*** Fix Logger.cpp compiler warning
** Adds: [[BamUtil: explainFlags|explainFlags]] - describes the SAM/BAM flags based on the flag value
** Update to [[BamUtil: stats|stats]]
*** Fix Stats to not try to not try to process a record after it is out of the loop (it would already have been processed or is invalid)
** Update to [[BamUtil: splitBam|splitBam]]
*** fix description of --noeof option
** Update to [[BamUtil: writeRegion|writeRegion]]
*** add exclude/required flags
** Update to [[BamUtil: dedup|dedup]] & [[BamUtil: recab|recab]]
*** Ignore secondary reads for dedup and making the recalibration table.
*** skip QC Failures
*** add excludeFlags parameters
** Update to [[BamUtil: clipOverlap|clipOverlap]]
*** add exclude flags
*** fix bug for readName sorted when a read is filtered due to flags
*** add sorting validation
** Update to [[BamUtil: bam2FastQ|bam2FastQ]]
*** add --merge option to generate interleaved files.
*** update to open the input file before opening the output files, so if there is an error, the outputs aren't opened
** Update to [[BamUtil: mergeBam|mergeBam]]
*** add option to ignore the RG PI field when checking headers
*** add more informative header merge error messages
'''Older Releases'''
'''Older Releases'''
* [[Media:BamUtil.1.0.9.tgz|BamUtil.1.0.9.tgz]] - Released 7/7/2013
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]] (version 1.0.7 should also work)
** Update to [[BamUtil: mergeBam|mergeBam]]
*** Update to ignore PG lines with duplicate IDs
*** Update to accept merges of matching RG lines
*** Update to log to stderr if no log/out file is specified
*[[Media:BamUtil.1.0.7.tgz|BamUtil.1.0.7.tgz]] - Released 1/29/2013
*[[Media:BamUtil.1.0.7.tgz|BamUtil.1.0.7.tgz]] - Released 1/29/2013
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]] or above
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]] or above
