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BamUtil

1,944 bytes added, 19:22, 2 January 2014
Releases
[[Media:BamUtilLibStatGen.1.0.910.tgztar.gz|BamUtilLibStatGen.1.0.910.tgz‎tar.gz‎]] - Released 71/72/20132014
'''BamUtilLibStatGen.1.0.9 10 Release Notes'''* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.910]] - see link for version updates* Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.910]]- see link for version updates* Update to [[BamUtil: mergeBam|mergeBam]]** Update to ignore PG lines with duplicate IDs** Update to accept merges of matching RG lines** Update to log to stderr if no logAdds PhoneHome/out file is specifiedVersion checking.
'''Older Releases'''
*[[Media:BamUtilLibStatGen.1.0.9.tgz|BamUtilLibStatGen.1.0.9.tgz‎]] - Released 7/7/2013** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]] ** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.9]]** Update to [[BamUtil: mergeBam|mergeBam]]*** Update to ignore PG lines with duplicate IDs*** Update to accept merges of matching RG lines*** Update to log to stderr if no log/out file is specified* There is no version 1.0.8. It was skipped to stya stay 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]]
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.1.0.910.tgztar.gz|BamUtil.1.0.910.tgz‎tar.gz‎]] - Released 71/72/20132014
'''BamUtil.1.0.9 10 Release Notes'''* [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz‎]] - Released 1/2/2014** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.910]] (** All*** Add PhoneHome/version 1checking*** Make sub-program names case independent*** Fix Logger.0.7 should also workcpp compiler warning** Adds: [[BamUtil: explainFlags|explainFlags]] - describes the SAM/BAM flags based on the flag value** Update to [[BamUtil: stats|stats]]*** Fix Stats to not try to not try to process a record after it is out of the loop (it would already have been processed or is invalid)** Update to [[BamUtil: mergeBamsplitBam|mergeBamsplitBam]]*** fix description of --noeof option** Update to ignore PG lines with duplicate IDs[[BamUtil: writeRegion|writeRegion]]*** add exclude/required flags** Update to [[BamUtil: dedup|dedup]] & [[BamUtil: recab|recab]]*** Ignore secondary reads for dedup and making the recalibration table.*** skip QC Failures*** add excludeFlags parameters** Update to accept merges of matching RG lines[[BamUtil: clipOverlap|clipOverlap]]*** add exclude flags*** fix bug for readName sorted when a read is filtered due to flags*** add sorting validation** Update to log [[BamUtil: bam2FastQ|bam2FastQ]]*** add --merge option to generate interleaved files.*** update to stderr open the input file before opening the output files, so if no log/out file there is specifiedan error, the outputs aren't opened** Update to [[BamUtil: mergeBam|mergeBam]]*** add option to ignore the RG PI field when checking headers*** add more informative header merge error messages
'''Older Releases'''
* [[Media:BamUtil.1.0.9.tgz|BamUtil.1.0.9.tgz‎]] - Released 7/7/2013
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]] (version 1.0.7 should also work)
** Update to [[BamUtil: mergeBam|mergeBam]]
*** Update to ignore PG lines with duplicate IDs
*** Update to accept merges of matching RG lines
*** Update to log to stderr if no log/out file is specified
 
*[[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

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