LibStatGen: BAM: Difference between revisions
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= SAM/BAM File= | = SAM/BAM File= | ||
See | See the github history: https://github.com/statgen/libStatGen/commits/master/bam for a list of the most recent updates to the BAM classes. | ||
[[BAM Review Action Items]] | [[BAM Review Action Items|Old BAM Review Action Items]] | ||
== Read & Write BAM/SAM Library Software == | == Read & Write BAM/SAM Library Software == | ||
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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. | ||
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| <code>[ | | <code>[http://www.sph.umich.edu/csg/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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Revision as of 14:26, 24 August 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. |
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
