Difference between revisions of "LibStatGen: BAM"
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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. | ||
|} | |} | ||
Revision as of 11:40, 7 September 2011
SAM/BAM File
See the github history: https://github.com/statgen/libStatGen/commits/master/bam for a list of the most recent updates to the BAM classes.
Read & Write BAM/SAM Library Software
The software reads the beginning of files opened for reading to determine if it is SAM/BAM. To determine the format (SAM/BAM) of files open for writing, the software checks the output file's extension. If the extension is "bam" it writes a BAM file, otherwise it writes a SAM file.
The library is found in statgen/lib/bam.
BAM/SAM Classes
| Class Name | Description |
|---|---|
SamFile
|
Class used for reading/writing SAM/BAM files and their headers and records. |
SamFileHeader
|
Class used for storing the header. Allows access for getting and setting header values when both reading & writing SAM/BAM files. |
SamHeaderRecord
|
Class used for storing the tag/value pairs within a given header line. |
SamRecord
|
Class used for storing a SAM/BAM Record. Allows access for getting and setting record values when both reading & writing SAM/BAM files. |
SamStatus
|
Status value used by the BAM classes for returning the status of the operations. |
SamValidator
|
Validates a SAM/BAM Record. |
SamValidationError
|
Validation Error Information for a SamRecord. |
SamValidationErrors
|
Container for ValidationErrors. |
Pileup
|
Template for doing pileups. |
PileupElement
|
Base class that can be used for the elements stored in a Pileup. |
ErrorHandler
|
Class for handling errors based on the error handling type. |
PosList
|
Store refID/position, but does not store values < 0. |
SamFilter
|
Class for filtering a SAM/BAM record. |
SamFlag
|
Class for getting information from a SAM/BAM flag. |
SamReferenceInfo
|
Class for tracking the reference information mapping between the reference ids and the reference names. |
SamTags
|
Class for parsing/creating/operating on SAM/BAM record tags. |
FAQs
Usage Examples
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.
Suggested Improvements/Features
For the latest changes, look at the history on github: https://github.com/statgen/libStatGen/commits/master/bam
See Old Change Log
