LibStatGen: BAM - Revision history

Ppwhite: /* BAM/SAM Classes */

2017-02-02T14:55:19Z

BAM/SAM Classes

Mktrost: /* Suggested Improvements/Features */

2012-06-12T12:58:32Z

Suggested Improvements/Features

← Older revision		Revision as of 08:58, 12 June 2012
Line 79:		Line 79:

	BamUtil contains a set of programs that uses this library to operate on SAM & BAM files. It includes tools for converting between SAM & BAM and validating the files. See [[BamUtil]] for more information and a description of all the tools.		BamUtil contains a set of programs that uses this library to operate on SAM & BAM files. It includes tools for converting between SAM & BAM and validating the files. See [[BamUtil]] for more information and a description of all the tools.


	~~== Suggested Improvements/Features ==~~
	~~For the latest changes, look at the history on github: https://github.com/statgen/libStatGen/commits/master/bam~~

Mktrost: /* Suggested Improvements/Features */

2012-06-12T12:58:16Z

Suggested Improvements/Features

← Older revision		Revision as of 08:58, 12 June 2012
Line 83:		Line 83:
	== Suggested Improvements/Features ==		== Suggested Improvements/Features ==
	For the latest changes, look at the history on github: https://github.com/statgen/libStatGen/commits/master/bam		For the latest changes, look at the history on github: https://github.com/statgen/libStatGen/commits/master/bam

	~~See [[C++ Library: BAM Change Log#Known Issues\|Old Change Log]]~~

Mktrost: Add rest of sam classes

2011-09-07T15:40:41Z

Add rest of sam classes

@@ Line 43: / Line 43: @@
 | <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code>
 | Container for ValidationErrors.
 |}

Mktrost: /* Suggested Improvements/Features */ Add link to github history

2011-09-07T13:12:36Z

Suggested Improvements/Features: Add link to github history

← Older revision		Revision as of 09:12, 7 September 2011
Line 58:		Line 58:

	== Suggested Improvements/Features ==		== Suggested Improvements/Features ==
	See [[C++ Library: BAM Change Log#Known Issues\|Change Log]]		For the latest changes, look at the history on github: https://github.com/statgen/libStatGen/commits/master/bam

			See [[C++ Library: BAM Change Log#Known Issues\|Old Change Log]]

Mktrost: Update Executable description

2011-09-07T12:30:22Z

Update Executable description

← Older revision		Revision as of 08:30, 7 September 2011
Line 28:		Line 28:
	\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>
	\| Class used for storing the tag/value pairs within a given header line.		\| Class used for storing the tag/value pairs within a given header line.
	\|}


	~~'''The documentation for the following classes still needs to be updated.'''~~
	~~{\| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"~~
	~~\|-style="background: #f2f2f2; text-align: center;"~~
	~~! Class Name !! Description~~
	\|-		\|-
	\| <code>[[C++ Class: SamRecord\|SamRecord]]</code>		\| <code>[[C++ Class: SamRecord\|SamRecord]]</code>
Line 59:		Line 52:


	== ~~Executable~~ ==		== Programs ==
	~~An executable~~ that ~~converts~~ between SAM ~~and~~ BAM ~~formats~~ and ~~that can validate SAM/BAM Records has been developed:~~ [[~~C++ Executable: bam\|bam~~]] and ~~specifically [[BamValidator]]~~
			BamUtil contains a set of programs that uses this library to operate on SAM & BAM files. It includes tools for converting between SAM & BAM and validating the files. See [[BamUtil]] for more information and a description of all the tools.


	== Suggested Improvements/Features ==		== Suggested Improvements/Features ==
	See [[C++ Library: BAM Change Log#Known Issues\|Change Log]]		See [[C++ Library: BAM Change Log#Known Issues\|Change Log]]

Mktrost: Update links for SamValidation to doxygen

2011-09-06T21:54:12Z

Update links for SamValidation to doxygen

← Older revision		Revision as of 17:54, 6 September 2011
Line 42:		Line 42:
	\| Status value used by the BAM classes for returning the status of the operations.		\| Status value used by the BAM classes for returning the status of the operations.
	\|-		\|-
	\| <code>[~~[C++ Class~~: SamValidator~~\|SamValidator]~~]</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamValidator.html SamValidator]</code>
	\| Validates a SAM/BAM Record.		\| Validates a SAM/BAM Record.
	\|-		\|-
	\| <code>[~~[C++ Class~~: SamValidationError~~\|SamValidationError]~~]</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamValidationError.html SamValidationError]</code>
	\| Validation Error Information for a SamRecord.		\| Validation Error Information for a SamRecord.
	\|-		\|-
	\| <code>[~~[C++ Class~~: SamValidationErrors~~\|SamValidationErrors]~~]</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code>
	\| Container for ValidationErrors.		\| Container for ValidationErrors.
	\|}		\|}

Mktrost at 21:14, 6 September 2011

2011-09-06T21:14:08Z

← Older revision		Revision as of 17:14, 6 September 2011
Line 39:		Line 39:
	\| Class used for storing a SAM/BAM Record. Allows access for getting and setting record values when both reading & writing SAM/BAM files.		\| Class used for storing a SAM/BAM Record. Allows access for getting and setting record values when both reading & writing SAM/BAM files.
	\|-		\|-
	\| <code>[~~[C++ Class~~: SamStatus~~\|SamStatus]~~]</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamStatus.html SamStatus]</code>
	\| Status value used by the BAM classes for returning the status of the operations.		\| Status value used by the BAM classes for returning the status of the operations.
	\|-		\|-

Mktrost at 22:12, 24 August 2011

2011-08-24T22:12:24Z

← Older revision		Revision as of 18:12, 24 August 2011
Line 28:		Line 28:
	\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>
	\| Class used for storing the tag/value pairs within a given header line.		\| Class used for storing the tag/value pairs within a given header line.
			\|}


			'''The documentation for the following classes still needs to be updated.'''
			{\| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
			\|-style="background: #f2f2f2; text-align: center;"
			! Class Name !! Description
	\|-		\|-
	\| <code>[[C++ Class: SamRecord\|SamRecord]]</code>		\| <code>[[C++ Class: SamRecord\|SamRecord]]</code>

Mktrost at 18:26, 24 August 2011

2011-08-24T18:26:18Z

← Older revision		Revision as of 14:26, 24 August 2011
Line 5:		Line 5:
	= SAM/BAM File=		= SAM/BAM File=

	See ~~[[C++ Library~~: ~~BAM Change Log]]~~ for a list of the most recent updates to the BAM classes.		See the github history: https://github.com/statgen/libStatGen/commits/master/bam for a list of the most recent updates to the BAM classes.

	[[BAM Review Action Items]]		[[BAM Review Action Items\|Old BAM Review Action Items]]

	== Read & Write BAM/SAM Library Software ==		== Read & Write BAM/SAM Library Software ==
Line 26:		Line 26:
	\| Class used for storing the header. Allows access for getting and setting header values when both reading & writing SAM/BAM files.		\| Class used for storing the header. Allows access for getting and setting header values when both reading & writing SAM/BAM files.
	\|-		\|-
	\| <code>[~~[C++ Class~~: SamHeaderRecord~~\|SamHeaderRecord]~~]</code>		\| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>
	\| Class used for storing the tag/value pairs within a given header line.		\| Class used for storing the tag/value pairs within a given header line.
	\|-		\|-

← Older revision		Revision as of 10:55, 2 February 2017
Line 26:		Line 26:
	\| Class used for storing the header. Allows access for getting and setting header values when both reading & writing SAM/BAM files.		\| Class used for storing the header. Allows access for getting and setting header values when both reading & writing SAM/BAM files.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</code>
	\| Class used for storing the tag/value pairs within a given header line.		\| Class used for storing the tag/value pairs within a given header line.
	\|-		\|-
Line 32:		Line 32:
	\| Class used for storing a SAM/BAM Record. Allows access for getting and setting record values when both reading & writing SAM/BAM files.		\| Class used for storing a SAM/BAM Record. Allows access for getting and setting record values when both reading & writing SAM/BAM files.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamStatus.html SamStatus]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamStatus.html SamStatus]</code>
	\| Status value used by the BAM classes for returning the status of the operations.		\| Status value used by the BAM classes for returning the status of the operations.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamValidator.html SamValidator]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidator.html SamValidator]</code>
	\| Validates a SAM/BAM Record.		\| Validates a SAM/BAM Record.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamValidationError.html SamValidationError]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidationError.html SamValidationError]</code>
	\| Validation Error Information for a SamRecord.		\| Validation Error Information for a SamRecord.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code>
	\| Container for ValidationErrors.		\| Container for ValidationErrors.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classPileup.html Pileup]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPileup.html Pileup]</code>
	\| Template for doing pileups.		\| Template for doing pileups.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classPileupElement.html PileupElement]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPileupElement.html PileupElement]</code>
	\| Base class that can be used for the elements stored in a Pileup.		\| Base class that can be used for the elements stored in a Pileup.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classErrorHandler.html ErrorHandler]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classErrorHandler.html ErrorHandler]</code>
	\| Class for handling errors based on the error handling type.		\| Class for handling errors based on the error handling type.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classPosList.html PosList]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPosList.html PosList]</code>
	\| Store refID/position, but does not store values < 0.		\| Store refID/position, but does not store values < 0.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamFilter.html SamFilter]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFilter.html SamFilter]</code>
	\| Class for filtering a SAM/BAM record.		\| Class for filtering a SAM/BAM record.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamFlag.html SamFlag]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFlag.html SamFlag]</code>
	\| Class for getting information from a SAM/BAM flag.		\| Class for getting information from a SAM/BAM flag.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamReferenceInfo.html SamReferenceInfo]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamReferenceInfo.html SamReferenceInfo]</code>
	\| Class for tracking the reference information mapping between the reference ids and the reference names.		\| Class for tracking the reference information mapping between the reference ids and the reference names.
	\|-		\|-
	\| <code>[http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/current/classSamTags.html SamTags]</code>		\| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamTags.html SamTags]</code>
	\| Class for parsing/creating/operating on SAM/BAM record tags.		\| Class for parsing/creating/operating on SAM/BAM record tags.
	\|}		\|}