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= bam Executable =
When the pipeline is compiled, the SAM/BAM executable, "bam" is generated in the pipeline/bam/ directory.
The software reads the beginning of an 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 bam executable has the following functions.
* [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]]
* [[C++ Executable: bam#Dump a BAM index file|Dump a BAM index file into an easy to read text version]]
* [[C++ Executable: bam#Read & Write indexed BAM file|Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file]]
This executable is built using the [[C++ Library: bam|bam library]].
== Read a SAM/BAM file and write as a SAM/BAM file ==
This executable takes 2 arguments. The first argument is the input file. The second argument is the output file. The executable converts the first file into the format of the second file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call:
./bam <bamFile>.bam <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.
=== Usage ===

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