Difference between revisions of "LibStatGen: BAM"
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[[Category:Software]] | [[Category:Software]] | ||
[[Category:C++]] | [[Category:C++]] | ||
| − | [[Category: | + | [[Category:BAM Classes]] |
= SAM/BAM File= | = SAM/BAM File= | ||
| − | See [[C++ Library: | + | See [[C++ Library: BAM Change Log]] for a list of the most recent updates to the BAM classes. |
[[BAM Review Action Items]] | [[BAM Review Action Items]] | ||
| − | == Read & Write BAM/SAM Library == | + | == 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 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 | + | The library is found in statgen/lib/bam. |
| − | + | === BAM/SAM Classes === | |
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== FAQs == | == FAQs == | ||
| − | [[SAM/BAM | + | [[SAM/BAM Classes FAQs]] |
== Usage Examples == | == Usage Examples == | ||
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== Suggested Improvements/Features == | == Suggested Improvements/Features == | ||
| − | See [[C++ Library: | + | See [[C++ Library: BAM Change Log#Known Issues|Change Log]] |
Revision as of 01:34, 2 November 2010
SAM/BAM File
See C++ Library: BAM Change Log 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 libbam 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
