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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. |
− | |}
| |
− |
| |
− |
| |
− | '''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> |
| | 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://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>[[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. |
| |- | | |- |
− | | <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. |
| |- | | |- |
− | | <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. |
| + | |- |
| + | | <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPileup.html Pileup]</code> |
| + | | Template for doing pileups. |
| + | |- |
| + | | <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. |
| + | |- |
| + | | <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classErrorHandler.html ErrorHandler]</code> |
| + | | Class for handling errors based on the error handling type. |
| + | |- |
| + | | <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classPosList.html PosList]</code> |
| + | | Store refID/position, but does not store values < 0. |
| + | |- |
| + | | <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFilter.html SamFilter]</code> |
| + | | Class for filtering a SAM/BAM record. |
| + | |- |
| + | | <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamFlag.html SamFlag]</code> |
| + | | Class for getting information from a SAM/BAM flag. |
| + | |- |
| + | | <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. |
| + | |- |
| + | | <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classSamTags.html SamTags]</code> |
| + | | Class for parsing/creating/operating on SAM/BAM record tags. |
| |} | | |} |
| | | |
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| | | |
− | == 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]]
| |
| | | |
− | == Suggested Improvements/Features ==
| + | 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]] | |