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− | [[Media:BamUtilLibStatGen.1.0.9.tgz|BamUtilLibStatGen.1.0.9.tgz]] - Released 7/7/2013 | + | [[Media:BamUtilLibStatGen.1.0.10.tar.gz|BamUtilLibStatGen.1.0.10.tar.gz]] - Released 1/2/2014 |
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− | '''BamUtilLibStatGen.1.0.9 Release Notes''' | + | '''BamUtilLibStatGen.1.0.10 Release Notes''' |
− | * Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]] | + | * Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]] - see link for version updates |
− | * Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.9]] | + | * Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.10]] - see link for version updates |
− | * Update to [[BamUtil: mergeBam|mergeBam]] | + | * Adds PhoneHome/Version checking. |
− | ** Update to ignore PG lines with duplicate IDs
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− | ** Update to accept merges of matching RG lines
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− | ** Update to log to stderr if no log/out file is specified
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| '''Older Releases''' | | '''Older Releases''' |
− | * There is no version 1.0.8. It was skipped to stya in line with libStatGen versions (libStatGen 1.0.8 added vcf support) | + | *[[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 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 | | *[[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]] | | ** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]] |
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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.1.0.9.tgz|BamUtil.1.0.9.tgz]] - Released 7/7/2013 | + | * [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz]] - Released 1/2/2014 |
| | | |
− | '''BamUtil.1.0.9 Release Notes''' | + | '''BamUtil.1.0.10 Release Notes''' |
− | * Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.9]] (version 1.0.7 should also work) | + | * [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz]] - Released 1/2/2014 |
− | * Update to [[BamUtil: mergeBam|mergeBam]] | + | ** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]] |
− | ** Update to ignore PG lines with duplicate IDs | + | ** All |
− | ** Update to accept merges of matching RG lines | + | *** Add PhoneHome/version checking |
− | ** Update to log to stderr if no log/out file is specified | + | *** Make sub-program names case independent |
| + | *** Fix Logger.cpp 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: splitBam|splitBam]] |
| + | *** fix description of --noeof option |
| + | ** Update to [[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 [[BamUtil: clipOverlap|clipOverlap]] |
| + | *** add exclude flags |
| + | *** fix bug for readName sorted when a read is filtered due to flags |
| + | *** add sorting validation |
| + | ** Update to [[BamUtil: bam2FastQ|bam2FastQ]] |
| + | *** add --merge option to generate interleaved files. |
| + | *** update to open the input file before opening the output files, so if there is an 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 |
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| | | |
| '''Older Releases''' | | '''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 | | *[[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 | | ** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]] or above |