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BamUtil

1,866 bytes added, 20:38, 29 January 2013
Releases
[[Media:BamUtilLibStatGen.1.0.67.tgz|BamUtilLibStatGen.1.0.67.tgz‎]] - Released 111/1429/2012 '''BamUtilLibStatGen.1.0.6 Release Notes'''* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.6]] * Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.6]]* Update to [[BamUtil: trimBam|trimBam]]** Update to allow trimming a different number of bases from each end of the read2013
'''BamUtilLibStatGen.1.0.7 Release Notes'''
* 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
'''Older Releases'''
*[[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: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.6]]
** Update to [[BamUtil: trimBam|trimBam]]
*** Update to allow trimming a different number of bases from each end of the read
*[[Media:BamUtilLibStatGen.1.0.5.tgz|BamUtilLibStatGen.1.0.5.tgz‎]] - Released 10/24/2012
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.5]]
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.1.0.67.tgz|BamUtil.1.0.67.tgz‎]] - Released 111/1429/20122013 '''BamUtil.1.0.7 Release Notes'''* 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
'''BamUtil.1.0.6 Release Notes'''
* Update to [[BamUtil: trimBam|trimBam]]
** Update to allow trimming a different number of bases from each end of the read
'''Older Releases'''
*[[Media:BamUtil.1.0.6.tgz|BamUtil.1.0.6.tgz‎]] - Released 11/14/2012
** Update to [[BamUtil: trimBam|trimBam]]
*** Update to allow trimming a different number of bases from each end of the read
*[[Media:BamUtil.1.0.5.tgz|BamUtil.1.0.5.tgz‎]] - Released 10/24/2012
** Update to [[BamUtil: dedup|dedup]]

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