Changes

From Genome Analysis Wiki
Jump to: navigation, search

BamUtil

1,007 bytes added, 17:12, 24 October 2012
Releases
[[Media:BamUtilLibStatGen.1.0.35.tgz|BamUtilLibStatGen.1.0.35.tgz‎]] - Released 0910/1924/2012
'''BamUtilLibStatGen.1.0.3 5 Release Notes'''* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.35]] * Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.35]]** AddsUpdates to: [[BamUtil: dedup|dedup]] , [[BamUtil: polishBam|polishBam]], [[BamUtil: recab|recab]]*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
'''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
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.2]]
** Adds leftShifting to [[BamUtil: writeRegion|writeRegion]] and [[BamUtil: convert|convert]]
** Adds more diff fields to [[BamUtil: diff|diff]]
 
* [[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.
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.1.0.35.tgz|BamUtil.1.0.35.tgz‎]] - Released 0910/1924/2012
'''BamUtil.1.0.3 5 Release Notes'''* Adds: 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
** Update Logger to write add compile option to stderr if output is stdout* Update to [[BamUtil: stats|stats]]** Add required/exclude flags** Exclude Clips if excluding umapped** Add --withinRegion flag** Update phredcompile without C++0x/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 libStatGenC++11
'''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
** Adds: [[BamUtil: bam2FastQ|bam2FastQ]]

Navigation menu