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| 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.
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| <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.
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|-
| 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.
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|-
| <code>[[C++ Class: SamStatus|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.
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|-
| <code>[[C++ Class: SamValidator|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.
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|-
| <code>[[C++ Class: SamValidationError|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.
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|-
| <code>[[C++ Class: SamValidationErrors|SamValidationErrors]]</code>
| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code>
| Container for ValidationErrors.
| Container for ValidationErrors.
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPileup.html Pileup]</code>
| Template for doing pileups.
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| <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.
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classErrorHandler.html ErrorHandler]</code>
| Class for handling errors based on the error handling type.
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPosList.html PosList]</code>
| Store refID/position, but does not store values < 0.
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFilter.html SamFilter]</code>
| Class for filtering a SAM/BAM record.
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFlag.html SamFlag]</code>
| Class for getting information from a SAM/BAM flag.
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| <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.
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamTags.html SamTags]</code>
| Class for parsing/creating/operating on SAM/BAM record tags.
|}
|}
== Executable ==
== Programs ==
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.
See [[C++ Library: BAM Change Log#Known Issues|Change Log]]
