Difference between revisions of "LibStatGen: BAM"
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The library is found in pipeline/bam, and is called libbam.a. | The library is found in pipeline/bam, and is called libbam.a. | ||
− | This library is dependent on two other libraries | + | This library is dependent on two other libraries: |
+ | # [[C++ Library: libcsg|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 | <path to base pipeline directory>/libbam.a <path to base pipeline directory>/libcsg/libcsg.a <path to base pipeline directory>/thirdParty/samtools/libbam.a | ||
Revision as of 16:22, 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. |