BamUtil - Revision history

Hmkang at 21:14, 11 September 2021

2021-09-11T21:14:59Z

← Older revision		Revision as of 17:14, 11 September 2021
Line 10:		Line 10:
	== Getting Help ==		== Getting Help ==

	If you have any questions please use the [~~http~~://~~groups.google~~.com/~~group~~/~~bamUtils~~ bamUtil ~~Google Group~~] to ~~ask questions or recommend improvements to bamUtil.~~		If you have any questions please use the [https://github.com/statgen/bamUtil bamUtil GitHub page] to raise and issue.

	~~Alternatively, you can e-mail me, Mary Kate Wing, at mktrost@umich.edu~~.

	See [[BamUtil: FAQ]] to see if your question has already been answered.		See [[BamUtil: FAQ]] to see if your question has already been answered.

Mktrost at 01:46, 31 July 2018

2018-07-31T01:46:22Z

← Older revision		Revision as of 21:46, 30 July 2018
Line 255:		Line 255:
	**Initial release of just bamUtil. It started from the tool found in the deprecated StatGen repository.		**Initial release of just bamUtil. It started from the tool found in the deprecated StatGen repository.
	**Contains: [[BamUtil: validate\|validate]], [[BamUtil: convert\|convert]], [[BamUtil: dumpHeader\|dumpHeader]], [[BamUtil: splitChromosome\|splitChromosome]], [[BamUtil: writeRegion\|writeRegion]], [[BamUtil: dumpRefInfo\|dumpRefInfo]], [[BamUtil: dumpIndex\|dumpIndex]], [[BamUtil: readIndexedBam\|readIndexedBam]], [[BamUtil: filter\|filter]], [[BamUtil: readReference\|readReference]], [[BamUtil: revert\|revert]], [[BamUtil: diff\|diff]], [[BamUtil: squeeze\|squeeze]], [[BamUtil: findCigars\|findCigars]], [[BamUtil: stats\|stats]]		**Contains: [[BamUtil: validate\|validate]], [[BamUtil: convert\|convert]], [[BamUtil: dumpHeader\|dumpHeader]], [[BamUtil: splitChromosome\|splitChromosome]], [[BamUtil: writeRegion\|writeRegion]], [[BamUtil: dumpRefInfo\|dumpRefInfo]], [[BamUtil: dumpIndex\|dumpIndex]], [[BamUtil: readIndexedBam\|readIndexedBam]], [[BamUtil: filter\|filter]], [[BamUtil: readReference\|readReference]], [[BamUtil: revert\|revert]], [[BamUtil: diff\|diff]], [[BamUtil: squeeze\|squeeze]], [[BamUtil: findCigars\|findCigars]], [[BamUtil: stats\|stats]]

			== Citation ==
			If you use BamUtil, please cite our publication on GotCloud which includes BamUtil:
			[http://genome.cshlp.org/content/early/2015/04/14/gr.176552.114.abstract Jun, Goo, et al. "An efficient and scalable analysis framework for variant extraction and refinement from population scale DNA sequence data." Genome research (2015): gr-176552.]


	= Programs =		= Programs =

Mktrost: /* Full Release (includes libStatGen) */

2017-11-13T03:55:56Z

Full Release (includes libStatGen)

← Older revision		Revision as of 23:55, 12 November 2017
Line 29:		Line 29:
	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.

			For version 1.0.14 and later, please download libStatGen and bamUtil separately:

	~~[[Media:BamUtilLibStatGen.1.0.13.tgz\|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015~~

	'''~~BamUtilLibStatGen.~~1.0.~~13 Release Notes~~'''		'''Version 1.0.14 - Released 7/8/2015'''
	* ~~Contains:~~ [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]] ~~- see link for version updates~~		*[[LibStatGen Download#Official Releases\|libStatGen version 1.0.14]]
	* ~~Contains:~~ [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.13]] ~~- see link for version updates~~		*[[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.14]]


	'''Older Releases'''		'''Older Releases'''
			* [[Media:BamUtilLibStatGen.1.0.13.tgz\|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015
			** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]] - see link for version updates
			** Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.13]] - see link for version updates


	* [[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014		* [[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
	** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates		** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates
Line 43:		Line 48:
	** Adds regions to [[BamUtil: mergeBam\|mergeBam]]		** Adds regions to [[BamUtil: mergeBam\|mergeBam]]
	** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]		** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]


	*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014		*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014

Mktrost: /* Release of just BamUtil (does not include libStatGen) */

2017-11-13T03:49:26Z

Release of just BamUtil (does not include libStatGen)

← Older revision		Revision as of 23:49, 12 November 2017
Line 111:		Line 111:
	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.

	'''BamUtil.1.0.13 Release Notes'''		'''BamUtil.1.0.14 Release Notes'''
			* BamUtil Version 1.0.14 - Released 7/8/2015
			** https://github.com/statgen/bamUtil/archive/v1.0.14.tar.gz
			** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.14]]
			** Update [[BamUtil: trimBam\|trimBam]]
			*** Add option to soft clip (-c) instead of trimming
			** Update [[BamUtil: clipOverlap\|clipOverlap]]
			*** Add option to mark reads as unmapped if they are entirely clipped
			** Update to [[BamUtil: bam2FastQ\|bam2FastQ]]
			*** Add option to gzip the output files
			*** Add option to split Read Groups into separate fastq files
			*** Add option to get the quality from a tag
			** Update [[BamUtil: recab\|recab]]
			*** Update to ignore ref 'N' when building the recalibration table
			*** Add ability to bin
			** Add Dedup_LowMem tool

			'''Older Releases'''
	* BamUtil Version 1.0.13 - Released 2/20/2015		* BamUtil Version 1.0.13 - Released 2/20/2015
	** https://github.com/statgen/bamUtil/archive/v1.0.13.tar.gz		** https://github.com/statgen/bamUtil/archive/v1.0.13.tar.gz
	** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]]		** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]]
	** ~~Makefule~~ Updates		** Makefile Updates
	*** Improve logic to determine actual path for the library		*** Improve logic to determine actual path for the library
	*** Update to append to USER_COMPILE_VARS even if specified on the command line		*** Update to append to USER_COMPILE_VARS even if specified on the command line
Line 127:		Line 144:
	*** Fix MD5sum calculation to convert fasta to uppercase prior to calculating		*** Fix MD5sum calculation to convert fasta to uppercase prior to calculating

	~~'''Older Releases'''~~
	* [[Media:BamUtil.1.0.12.tgz\|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014		* [[Media:BamUtil.1.0.12.tgz\|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014
	** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]]		** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]]

Mktrost: /* Full Release (includes libStatGen) */

2015-02-20T16:17:18Z

Full Release (includes libStatGen)

← Older revision		Revision as of 12:17, 20 February 2015
Line 30:		Line 30:


	[[Media:BamUtilLibStatGen.1.0.13.~~tar.gz~~\|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015		[[Media:BamUtilLibStatGen.1.0.13.tgz\|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015

	'''BamUtilLibStatGen.1.0.13 Release Notes'''		'''BamUtilLibStatGen.1.0.13 Release Notes'''

Mktrost: /* Full Release (includes libStatGen) */

2015-02-20T16:12:56Z

Full Release (includes libStatGen)

← Older revision		Revision as of 12:12, 20 February 2015
Line 30:		Line 30:


	[[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/~~2014~~		[[Media:BamUtilLibStatGen.1.0.13.tar.gz\|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015

	'''BamUtilLibStatGen.1.0.12 Release Notes'''		'''BamUtilLibStatGen.1.0.13 Release Notes'''
	* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates		* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]] - see link for version updates
	* Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.12]] - see link for version updates		* Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.13]] - see link for version updates
	* Adds regions to [[BamUtil: mergeBam\|mergeBam]]
	* Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]


	'''Older Releases'''		'''Older Releases'''
			* [[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
			** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates
			** Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.12]] - see link for version updates
			** Adds regions to [[BamUtil: mergeBam\|mergeBam]]
			** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]


	*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014		*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014
	** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.11]] - see link for version updates		** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.11]] - see link for version updates

Mktrost: /* Release of just BamUtil (does not include libStatGen) */

2015-02-20T15:43:40Z

Release of just BamUtil (does not include libStatGen)

← Older revision		Revision as of 11:43, 20 February 2015
Line 106:		Line 106:
	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~~.1.0.12.~~tgz~~\|~~BamUtil.~~1.0.~~12.tgz‎~~]] - ~~Released 5/14/2014~~		'''BamUtil.1.0.13 Release Notes'''
			* BamUtil Version 1.0.13 - Released 2/20/2015
			** https://github.com/statgen/bamUtil/archive/v1.0.13.tar.gz
			** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]]
			** Makefule Updates
			*** Improve logic to determine actual path for the library
			*** Update to append to USER_COMPILE_VARS even if specified on the command line
			** Update [[BamUtil: writeRegion\|writeRegion]]
			*** Add option to specify readnames to keep in a file
			*** Fixed bug that if a read overlapped 2 BED positions, it was printed twice
			** Update to [[BamUtil: bam2FastQ\|bam2FastQ]]
			*** Update to skip non-primary reads
			** Update to [[BamUtil: polishBam\|polishBam]]
			*** Update to handle '\t' string inputs and to add CO option
			*** Fix MD5sum calculation to convert fasta to uppercase prior to calculating

	'''~~BamUtil.1.0.12 Release Notes~~'''		'''Older Releases'''
	* [[Media:BamUtil.1.0.12.tgz\|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014		* [[Media:BamUtil.1.0.12.tgz\|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014
	** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]]		** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]]
Line 115:		Line 129:
	** Update to [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], [[BamUtil: diff\|diff]]		** Update to [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], [[BamUtil: diff\|diff]]
	*** Also accept ',' instead of just ';' as the delimiter in the input tags string.		*** Also accept ',' instead of just ';' as the delimiter in the input tags string.

	~~'''Older Releases'''~~

	* [[Media:BamUtil.1.0.11.tgz\|BamUtil.1.0.11.tgz‎]] - Released 2/28/2014		* [[Media:BamUtil.1.0.11.tgz\|BamUtil.1.0.11.tgz‎]] - Released 2/28/2014

Mktrost: /* Full Release (includes libStatGen) */

2014-05-14T14:47:49Z

Full Release (includes libStatGen)

← Older revision		Revision as of 10:47, 14 May 2014
Line 35:		Line 35:
	* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates		* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates
	* Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.12]] - see link for version updates		* Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.12]] - see link for version updates
	* Adds regions to mergeBam		* Adds regions to [[BamUtil: mergeBam\|mergeBam]]
	* Accept ',' delimiters for the tags string input in squeeze, revert, & diff		* Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]

Mktrost: /* Releases */

2014-05-14T14:45:38Z

Releases

← Older revision		Revision as of 10:45, 14 May 2014
Line 30:		Line 30:


	[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.~~tar.gz‎~~]] - Released 2/28/2014		[[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014

	'''BamUtilLibStatGen.1.0.11 Release Notes'''		'''BamUtilLibStatGen.1.0.12 Release Notes'''
	* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.11]] - see link for version updates		* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates
	* Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.11]] - see link for version updates		* Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.12]] - see link for version updates
	* ~~Now properly supports~~ 'B' & ~~'f' tags~~		* Adds regions to mergeBam
	* Cleanup - compile issues		* Accept ',' delimiters for the tags string input in squeeze, revert, & diff


	'''Older Releases'''		'''Older Releases'''
			*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014
			** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.11]] - see link for version updates
			** Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.11]] - see link for version updates
			** Now properly supports 'B' & 'f' tags
			** Cleanup - compile issues

	*[[Media:BamUtilLibStatGen.1.0.10.tar.gz\|BamUtilLibStatGen.1.0.10.tar.gz‎]] - Released 1/2/2014		*[[Media:BamUtilLibStatGen.1.0.10.tar.gz\|BamUtilLibStatGen.1.0.10.tar.gz‎]] - Released 1/2/2014
	** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.10]] - see link for version updates		** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.10]] - see link for version updates
Line 100:		Line 106:
	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.1.0.11.tgz\|BamUtil.1.0.11.tgz‎]] - Released 2/28/2014		* [[Media:BamUtil.1.0.12.tgz\|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014

			'''BamUtil.1.0.12 Release Notes'''
			* [[Media:BamUtil.1.0.12.tgz\|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014
			** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]]
			** Update [[BamUtil: mergeBam\|mergeBam]]
			*** Add a regions option
			** Update to [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], [[BamUtil: diff\|diff]]
			*** Also accept ',' instead of just ';' as the delimiter in the input tags string.

			'''Older Releases'''

	~~'''BamUtil.1.0.11 Release Notes'''~~
	* [[Media:BamUtil.1.0.11.tgz\|BamUtil.1.0.11.tgz‎]] - Released 2/28/2014		* [[Media:BamUtil.1.0.11.tgz\|BamUtil.1.0.11.tgz‎]] - Released 2/28/2014
	** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.11]]		** Requires, but does not include: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.11]]
Line 114:		Line 129:
	*** Update compatibility with libStatGen due to 'B' & 'f' tag handling updates		*** Update compatibility with libStatGen due to 'B' & 'f' tag handling updates
	** Add tests for 'B' & 'f' tags		** Add tests for 'B' & 'f' tags


	~~'''Older Releases'''~~

	* [[Media:BamUtil.1.0.10.tar.gz\|BamUtil.1.0.10.tar.gz‎]] - Released 1/2/2014		* [[Media:BamUtil.1.0.10.tar.gz\|BamUtil.1.0.10.tar.gz‎]] - Released 1/2/2014

Mktrost: /* Getting Help */

2014-03-25T13:39:08Z

Getting Help

← Older revision		Revision as of 09:39, 25 March 2014
Line 14:		Line 14:
	Alternatively, you can e-mail me, Mary Kate Wing, at mktrost@umich.edu.		Alternatively, you can e-mail me, Mary Kate Wing, at mktrost@umich.edu.

			See [[BamUtil: FAQ]] to see if your question has already been answered.

	== Where to Find It ==		== Where to Find It ==

← Older revision		Revision as of 23:55, 12 November 2017
Line 29:		Line 29:
	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.

			For version 1.0.14 and later, please download libStatGen and bamUtil separately:

	~~[[Media:BamUtilLibStatGen.1.0.13.tgz\|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015~~

	'''~~BamUtilLibStatGen.~~1.0.~~13 Release Notes~~'''		'''Version 1.0.14 - Released 7/8/2015'''
	* ~~Contains:~~ [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]] ~~- see link for version updates~~		*[[LibStatGen Download#Official Releases\|libStatGen version 1.0.14]]
	* ~~Contains:~~ [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.13]] ~~- see link for version updates~~		*[[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.14]]


	'''Older Releases'''		'''Older Releases'''
			* [[Media:BamUtilLibStatGen.1.0.13.tgz\|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015
			** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]] - see link for version updates
			** Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.13]] - see link for version updates


	* [[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014		* [[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
	** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates		** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates
Line 43:		Line 48:
	** Adds regions to [[BamUtil: mergeBam\|mergeBam]]		** Adds regions to [[BamUtil: mergeBam\|mergeBam]]
	** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]		** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]


	*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014		*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014

← Older revision		Revision as of 12:12, 20 February 2015
Line 30:		Line 30:


	[[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/~~2014~~		[[Media:BamUtilLibStatGen.1.0.13.tar.gz\|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015

	'''BamUtilLibStatGen.1.0.12 Release Notes'''		'''BamUtilLibStatGen.1.0.13 Release Notes'''
	* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates		* Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.13]] - see link for version updates
	* Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.12]] - see link for version updates		* Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.13]] - see link for version updates
	* Adds regions to [[BamUtil: mergeBam\|mergeBam]]
	* Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]


	'''Older Releases'''		'''Older Releases'''
			* [[Media:BamUtilLibStatGen.1.0.12.tar.gz\|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
			** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.12]] - see link for version updates
			** Contains: [[#Release of just BamUtil (does not include libStatGen)\|bamUtil version 1.0.12]] - see link for version updates
			** Adds regions to [[BamUtil: mergeBam\|mergeBam]]
			** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze\|squeeze]], [[BamUtil: revert\|revert]], & [[BamUtil: diff\|diff]]


	*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014		*[[Media:BamUtilLibStatGen.1.0.11.tar.gz\|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014
	** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.11]] - see link for version updates		** Contains: [[LibStatGen Download#Official Releases\|libStatGen version 1.0.11]] - see link for version updates