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= SAM/BAM File=
= SAM/BAM File=
== Reading/Writing SAM/BAM Files ==
== Read & Write BAM/SAM Executable ==
When the pipeline is compiled, the sam/bam executable, "bam" is generated in the pipeline/bam/ directory.
This executable takes 2 arguments. The first argument is the input file. The second argument is the output file.
From the pipeline/bam/ direcotry:
./bam initialBam.bam convertedToSam.sam
Don't forget to put in the paths to the executable and your test files.
== Reading/Writing SAM/BAM Files In Your Program ==
The SamFile class allows a user to easily read/write a SAM/BAM file.
The SamFile class allows a user to easily read/write a SAM/BAM file.
The methods found in this class are:
The methods found in this class are:
