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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 fix some compile issues on ubuntu 12.10
| + | * Update to [[BamUtil: mergeBam|mergeBam]] |
− | * Update use of SamRecord::getStringTag to expect the return of a const string pointer due to libStatGen v1.0.7 updates
| + | ** Update to ignore PG lines with duplicate IDs |
− | * Update SamReferenceInfo usage due to libStatGen v1.0.7 updates
| + | ** 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) | |
− | ** Rename RGMergeBam to MergeBam
| |
− | ** Update to handle files that already have an RG
| |
| | | |
| '''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]] |
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| 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 fix some compile issues on ubuntu 12.10
| + | * Update to [[BamUtil: mergeBam|mergeBam]] |
− | * Update use of SamRecord::getStringTag to expect the return of a const string pointer due to libStatGen v1.0.7 updates
| + | ** Update to ignore PG lines with duplicate IDs |
− | * Update SamReferenceInfo usage due to libStatGen v1.0.7 updates
| + | ** 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) | |
− | ** Rename RGMergeBam to MergeBam
| |
− | ** Update to handle files that already have an RG
| |
| | | |
| | | |
| '''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]] |