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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. |
| |- | | |- |
− | | <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. |
| |- | | |- |
− | | <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. |
| |} | | |} |
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| | | |
| 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. |
− |
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− |
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− | == Suggested Improvements/Features ==
| |
− | 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]]
| |