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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 |
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− | '''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 |
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| '''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]] |
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| ** 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]] |
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| * [[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. |
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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. |
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− | [[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 |
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− | '''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 |
− | * Update to [[BamUtil: stats|stats]]
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− | ** Add required/exclude flags
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− | ** Exclude Clips if excluding umapped
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− | ** Add --withinRegion flag
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− | ** Update phred/qual counts to be uint64_t instead of int to avoid overflow
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− | * Update to [[BamUtil: validate|validate]]
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− | ** Detect header failures
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− | * Update to [[BamUtil: diff|diff]]
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− | ** Update to specify chromosome/pos in ZP as a string rather than int so both can be shown
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− | * Update to [[BamUtil: readReference|readReference]]
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− | ** Output error message if the reference name is not found
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− | * Update to [[BamUtil: splitChromosome|splitChromosome]]
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− | ** Update to actually split the chromosomes and not just hard coded to output chromosomes ids 0-22
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− | * Update Makefile to have cloneLib for cloning libStatGen
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| '''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]] |