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| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code>
| <code>[http://www.sph.umich.edu/csg/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>
| Template for doing pileups.
|-
| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classPileupElement.html PileupElement]</code>
| 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>
| Class for handling errors based on the error handling type.
|-
| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classPosList.html PosList]</code>
| Store refID/position, but does not store values < 0.
|-
| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamFilter.html SamFilter]</code>
| Class for filtering a SAM/BAM record.
|-
| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamFlag.html SamFlag]</code>
| Class for getting information from a SAM/BAM flag.
|-
| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamReferenceInfo.html SamReferenceInfo]</code>
| 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>
| Class for parsing/creating/operating on SAM/BAM record tags.
|}
|}
