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, 11:38, 17 March 2010
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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: |