Difference between revisions of "LibStatGen: BAM"
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| 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>[ | + | | <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamValidator.html SamValidator]</code> |
| Validates a SAM/BAM Record. | | Validates a SAM/BAM Record. | ||
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− | | <code>[ | + | | <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamValidationError.html SamValidationError]</code> |
| Validation Error Information for a SamRecord. | | Validation Error Information for a SamRecord. | ||
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− | | <code>[ | + | | <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamValidationErrors.html SamValidationErrors]</code> |
| Container for ValidationErrors. | | Container for ValidationErrors. | ||
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Revision as of 17:54, 6 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. |
The documentation for the following classes still needs to be updated.
Class Name | Description |
---|---|
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. |
FAQs
Usage Examples
Executable
An executable that converts between SAM and BAM formats and that can validate SAM/BAM Records has been developed: bam and specifically BamValidator
Suggested Improvements/Features
See Change Log