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BamUtil

1,169 bytes added, 18:16, 19 September 2012
Releases: Update new release
[[Media:BamUtilLibStatGen.1.0.23.tgz|BamUtilLibStatGen.1.0.23.tgz‎]] - Released 0509/1619/2012
'''BamUtilLibStatGen.1.0.2 3 Release Notes'''* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.23]] * Adds: [[BamUtil: bam2FastQdedup|bam2FastQdedup]] [[BamUtil: recab|recab]]
'''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
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.1]]
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.1.0.23.tgz|BamUtil.1.0.23.tgz‎]] - Released 0509/1619/2012 '''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'''
*[[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
** Adds: [[BamUtil: splitBam|splitBam]], [[BamUtil: clipOverlap|clipOverlap]], [[BamUtil: trimBam|trimBam]], [[BamUtil: polishBam|polishBam]], [[BamUtil: rgMergeBam|rgMergeBam]], [[BamUtil: gapInfo|gapInfo]]