Changes

From Genome Analysis Wiki
Jump to: navigation, search

BamUtil

1,011 bytes added, 11:30, 7 July 2013
Releases
[[Media:BamUtilLibStatGen.1.0.79.tgz|BamUtilLibStatGen.1.0.79.tgz‎]] - Released 17/297/2013
'''BamUtilLibStatGen.1.0.7 9 Release Notes'''* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.79]] * Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.79]]* 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: diffmergeBam|diffmergeBam]]** 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]]ignore PG lines with duplicate IDs** Update to facilitate adding other overlap handling functionsaccept merges of matching RG lines** Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)** Rename RGMergeBam to MergeBam** Update log to handle files that already have an RGstderr if no log/out file is specified
'''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
** 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.
*[[Media:BamUtil.1.0.79.tgz|BamUtil.1.0.79.tgz‎]] - Released 17/297/2013
'''BamUtil.1.0.7 9 Release Notes'''* Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.79]] 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(version 1.0.7 updates* Update SamReferenceInfo usage due to libStatGen v1.0.7 updatesshould also work)* Update to [[BamUtil: diffmergeBam|diffmergeBam]]** 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]]ignore PG lines with duplicate IDs** Update to facilitate adding other overlap handling functionsaccept merges of matching RG lines** Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)** Rename RGMergeBam to MergeBam** Update log to handle files that already have an RGstderr if no log/out file is specified
'''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
** Update to [[BamUtil: trimBam|trimBam]]

Navigation menu