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[[Media:BamUtilLibStatGen.1.0.3.tgz|BamUtilLibStatGen.1.0.3.tgz]] - Released 09/19/2012
[[Media:BamUtilLibStatGen.1.0.5.tgz|BamUtilLibStatGen.1.0.5.tgz]] - Released 10/24/2012
'''BamUtilLibStatGen.1.0.3 Release Notes'''
'''BamUtilLibStatGen.1.0.5 Release Notes'''
* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.3]]
* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.5]]
* Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.3]]
* Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.5]]
** Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]]
* Updates to: [[BamUtil: dedup|dedup]], [[BamUtil: polishBam|polishBam]], [[BamUtil: recab|recab]]
** See [[#Release of just BamUtil (does not include libStatGen)|below]] for additional details on updates
* Update to add compile option to compile without C++0x/C++11
* See [[#Release of just BamUtil (does not include libStatGen)|below]] for additional details on updates
'''Older Releases'''
'''Older Releases'''
*BamUtilLibStatGen.1.0.4.tgz - Released skipped
*[[Media:BamUtilLibStatGen.1.0.3.tgz|BamUtilLibStatGen.1.0.3.tgz]] - Released 09/19/2012
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.3]]
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.3]]
** Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]]
*[[Media:BamUtilLibStatGen.1.0.2.tgz|BamUtilLibStatGen.1.0.2.tgz]] - Released 05/16/2012
*[[Media:BamUtilLibStatGen.1.0.2.tgz|BamUtilLibStatGen.1.0.2.tgz]] - Released 05/16/2012
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.2]]
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.2]]
** Adds leftShifting to [[BamUtil: writeRegion|writeRegion]] and [[BamUtil: convert|convert]]
** Adds leftShifting to [[BamUtil: writeRegion|writeRegion]] and [[BamUtil: convert|convert]]
** Adds more diff fields to [[BamUtil: diff|diff]]
** Adds more diff fields to [[BamUtil: diff|diff]]
* [[Media:BamUtilLibStatGen.1.0.0.tgz|BamUtilLibStatGen.1.0.0.tgz]] - Released 10/10/2011
* [[Media:BamUtilLibStatGen.1.0.0.tgz|BamUtilLibStatGen.1.0.0.tgz]] - Released 10/10/2011
**Initial release of bamUtil that includes libStatGen version 1.0.0. It started from the tool found in the deprecated StatGen repository.
**Initial release of bamUtil that includes libStatGen version 1.0.0. It started from the tool found in the deprecated StatGen repository.
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.1.0.3.tgz|BamUtil.1.0.3.tgz]] - Released 09/19/2012
[[Media:BamUtil.1.0.5.tgz|BamUtil.1.0.5.tgz]] - Released 10/24/2012
'''BamUtil.1.0.3 Release Notes'''
'''BamUtil.1.0.5 Release Notes'''
* Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]]
* Update to [[BamUtil: dedup|dedup]]
** Update logic for which pair to keep if they have the same quality
* Update to [[BamUtil: polishBam|polishBam]]
** Update to print the number of successful header additions
* Update to [[BamUtil: recab|recab]]
** Update to print the number of base skipped due to the base quality
* General Updates
* General Updates
** Update Logger to write to stderr if output is stdout
** Update to add compile option to compile without C++0x/C++11
'''Older Releases'''
'''Older Releases'''
*BamUtil.1.0.4.tgz - Released skipped
*[[Media:BamUtil.1.0.3.tgz|BamUtil.1.0.3.tgz]] - Released 09/19/2012
** Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]]
** General Updates
*** Update Logger to write to stderr if output is stdout
** Update to [[BamUtil: stats|stats]]
*** Add required/exclude flags
*** Exclude Clips if excluding umapped
*** Add --withinRegion flag
*** Update phred/qual counts to be uint64_t instead of int to avoid overflow
** Update to [[BamUtil: validate|validate]]
*** Detect header failures
** Update to [[BamUtil: diff|diff]]
*** Update to specify chromosome/pos in ZP as a string rather than int so both can be shown
** Update to [[BamUtil: readReference|readReference]]
*** Output error message if the reference name is not found
** Update to [[BamUtil: splitChromosome|splitChromosome]]
*** Update to actually split the chromosomes and not just hard coded to output chromosomes ids 0-22
** Update Makefile to have cloneLib for cloning libStatGen
*[[Media:BamUtil.1.0.2.tgz|BamUtil.1.0.2.tgz]] - Released 05/16/2012
*[[Media:BamUtil.1.0.2.tgz|BamUtil.1.0.2.tgz]] - Released 05/16/2012
** Adds: [[BamUtil: bam2FastQ|bam2FastQ]]
** Adds: [[BamUtil: bam2FastQ|bam2FastQ]]
