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The software reads the beginning of the input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, 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 the input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension. If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.
== Read & Write BAM/SAM Library ==
The software for reading/writing/parsing/validating SAM/BAM files is also available in library format. The library is also 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
