Difference between revisions of "LibStatGen: BAM"
From Genome Analysis Wiki
Jump to navigationJump to searchLine 38: | Line 38: | ||
| <code>[[C++ Class: SamValidator|SamValidator]]</code> | | <code>[[C++ Class: SamValidator|SamValidator]]</code> | ||
| Validates a SAM/BAM Record. | | Validates a SAM/BAM Record. | ||
+ | |- | ||
+ | | <code>[[C++ Class: SamValidationError|SamValidationError]]</code> | ||
+ | | Validation Error Information for a SamRecord. | ||
+ | |- | ||
+ | | <code>[[C++ Class: SamValidationErrors|SamValidationErrors]]</code> | ||
+ | | Container for ValidationErrors. | ||
|} | |} | ||
== Suggested Improvements/Features == | == Suggested Improvements/Features == |
Revision as of 17:52, 11 May 2010
SAM/BAM File
See C++ Library: libbam Change Log for a list of the most recent updates to the library.
Read & Write BAM/SAM Library
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 pipeline/bam, and is called libbam.a.
This library is dependent on two other libraries:
- libcsg/libcsg.a
- thirdParty/samtools/libbam.a
Be sure to include them all in the proper order:
<path to base pipeline directory>/libbam.a <path to base pipeline directory>/libcsg/libcsg.a <path to base pipeline directory>/thirdParty/samtools/libbam.a
Classes in the BAM/SAM Library
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. |