Line 22: |
Line 22: |
| | | |
| | | |
− | [[Media:BamUtilLibStatGen.1.0.2.tgz|BamUtilLibStatGen.1.0.2.tgz]] - Released 05/16/2012 | + | [[Media:BamUtilLibStatGen.1.0.3.tgz|BamUtilLibStatGen.1.0.3.tgz]] - Released 09/19/2012 |
| | | |
− | '''BamUtilLibStatGen.1.0.2 Release Notes''' | + | '''BamUtilLibStatGen.1.0.3 Release Notes''' |
− | * Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.2]] | + | * Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.3]] |
− | * Adds: [[BamUtil: bam2FastQ|bam2FastQ]] | + | * Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]] |
| | | |
| | | |
| '''Older Releases''' | | '''Older Releases''' |
| + | *[[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]] |
| + | ** Adds: [[BamUtil: bam2FastQ|bam2FastQ]] |
| *[[Media:BamUtilLibStatGen.1.0.1.tgz|BamUtilLibStatGen.1.0.1.tgz]] - Released 05/04/2012 | | *[[Media:BamUtilLibStatGen.1.0.1.tgz|BamUtilLibStatGen.1.0.1.tgz]] - Released 05/04/2012 |
| ** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.1]] | | ** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.1]] |
Line 46: |
Line 49: |
| 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.1.0.2.tgz|BamUtil.1.0.2.tgz]] - Released 05/16/2012 | + | [[Media:BamUtil.1.0.3.tgz|BamUtil.1.0.3.tgz]] - Released 09/19/2012 |
| + | |
| + | '''BamUtil.1.0.3 Release Notes''' |
| + | * 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 |
| | | |
− | '''BamUtil.1.0.2 Release Notes'''
| |
− | * Adds: [[BamUtil: bam2FastQ|bam2FastQ]]
| |
| | | |
| '''Older Releases''' | | '''Older Releases''' |
| + | *[[Media:BamUtil.1.0.2.tgz|BamUtil.1.0.2.tgz]] - Released 05/16/2012 |
| + | ** Adds: [[BamUtil: bam2FastQ|bam2FastQ]] |
| *[[Media:BamUtil.1.0.1.tgz|BamUtil.1.0.1.tgz]] - Released 05/04/2012 | | *[[Media:BamUtil.1.0.1.tgz|BamUtil.1.0.1.tgz]] - Released 05/04/2012 |
| ** Adds: [[BamUtil: splitBam|splitBam]], [[BamUtil: clipOverlap|clipOverlap]], [[BamUtil: trimBam|trimBam]], [[BamUtil: polishBam|polishBam]], [[BamUtil: rgMergeBam|rgMergeBam]], [[BamUtil: gapInfo|gapInfo]] | | ** Adds: [[BamUtil: splitBam|splitBam]], [[BamUtil: clipOverlap|clipOverlap]], [[BamUtil: trimBam|trimBam]], [[BamUtil: polishBam|polishBam]], [[BamUtil: rgMergeBam|rgMergeBam]], [[BamUtil: gapInfo|gapInfo]] |