Difference between revisions of "LibStatGen: BAM"
From Genome Analysis Wiki
Jump to navigationJump to search| Line 1: | Line 1: | ||
= SAM/BAM File= | = SAM/BAM File= | ||
| − | [[C++ Library: bam Change Log]] | + | See [[C++ Library: bam Change Log]] for a list of the most recent updates to the library. |
| − | == Read & Write BAM/SAM | + | == 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, so be sure to include them all in the proper order: | This library is dependent on two other libraries, so be sure to include them all in the proper order: | ||
Revision as of 17:09, 6 April 2010
SAM/BAM File
See C++ Library: bam 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, so 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. |
SamRecord
|
Class used for storing a SAM/BAM Record. Allows access for getting and setting record values when both reading & writing SAM/BAM files. |
