Difference between revisions of "LibStatGen: BAM"
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| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classSamHeaderRecord.html SamHeaderRecord]</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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| <code>[[C++ Class: SamRecord|SamRecord]]</code> | | <code>[[C++ Class: SamRecord|SamRecord]]</code> | ||
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| − | == | + | == Programs == |
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| + | 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. | ||
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== Suggested Improvements/Features == | == Suggested Improvements/Features == | ||
See [[C++ Library: BAM Change Log#Known Issues|Change Log]] | See [[C++ Library: BAM Change Log#Known Issues|Change Log]] | ||
Revision as of 08:30, 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. |
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
See Change Log
