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[[Media:BamUtilLibStatGen.1.0.7.tgz|BamUtilLibStatGen.1.0.7.tgz]] - Released 1/29/2013
[[Media:BamUtilLibStatGen.1.0.9.tgz|BamUtilLibStatGen.1.0.9.tgz]] - Released 7/7/2013
'''BamUtilLibStatGen.1.0.7 Release Notes'''
'''BamUtilLibStatGen.1.0.9 Release Notes'''
* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]]
* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]]
* Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.7]]
* 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 [[BamUtil: diff|diff]]
** Update to log to stderr if no log/out file is specified
** Fix DIFF to test and properly handle running out of available records. Previously no message was printed when this happened and there was a bug for which file it freed
* Update to [[BamUtil: clipOverlap|clipOverlap]]
** Update to facilitate adding other overlap handling functions
* Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)
'''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.1.0.7.tgz|BamUtilLibStatGen.1.0.7.tgz]] - Released 1/29/2013
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]]
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.7]]
** Update to fix some compile issues on ubuntu 12.10
** Update use of SamRecord::getStringTag to expect the return of a const string pointer due to libStatGen v1.0.7 updates
** Update SamReferenceInfo usage due to libStatGen v1.0.7 updates
** Update to [[BamUtil: diff|diff]]
*** Fix DIFF to test and properly handle running out of available records. Previously no message was printed when this happened and there was a bug for which file it freed
** Update to [[BamUtil: clipOverlap|clipOverlap]]
*** Update to facilitate adding other overlap handling functions
** Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)
*** Rename RGMergeBam to MergeBam
*** Update to handle files that already have an RG
*[[Media:BamUtilLibStatGen.1.0.6.tgz|BamUtilLibStatGen.1.0.6.tgz]] - Released 11/14/2012
*[[Media:BamUtilLibStatGen.1.0.6.tgz|BamUtilLibStatGen.1.0.6.tgz]] - Released 11/14/2012
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.6]]
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.6]]
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.1.0.7.tgz|BamUtil.1.0.7.tgz]] - Released 1/29/2013
* [[Media:BamUtil.1.0.9.tgz|BamUtil.1.0.9.tgz]] - Released 7/7/2013
'''BamUtil.1.0.7 Release Notes'''
'''BamUtil.1.0.9 Release Notes'''
* 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 1.0.9]] (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 [[BamUtil: diff|diff]]
** Update to log to stderr if no log/out file is specified
** Fix DIFF to test and properly handle running out of available records. Previously no message was printed when this happened and there was a bug for which file it freed
* Update to [[BamUtil: clipOverlap|clipOverlap]]
** Update to facilitate adding other overlap handling functions
* Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)
'''Older Releases'''
'''Older Releases'''
*[[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
** Update to fix some compile issues on ubuntu 12.10
** Update use of SamRecord::getStringTag to expect the return of a const string pointer due to libStatGen v1.0.7 updates
** Update SamReferenceInfo usage due to libStatGen v1.0.7 updates
** Update to [[BamUtil: diff|diff]]
*** Fix DIFF to test and properly handle running out of available records. Previously no message was printed when this happened and there was a bug for which file it freed
** Update to [[BamUtil: clipOverlap|clipOverlap]]
*** Update to facilitate adding other overlap handling functions
** Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)
*** Rename RGMergeBam to MergeBam
*** Update to handle files that already have an RG
*[[Media:BamUtil.1.0.6.tgz|BamUtil.1.0.6.tgz]] - Released 11/14/2012
*[[Media:BamUtil.1.0.6.tgz|BamUtil.1.0.6.tgz]] - Released 11/14/2012
** Update to [[BamUtil: trimBam|trimBam]]
** Update to [[BamUtil: trimBam|trimBam]]
