Template:InBAMInputFile: Difference between revisions
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{{{hdr|==}}} input File (<code>--in</code>) {{{hdr|==}}} | {{{hdr|===}}} input File (<code>--in</code>) {{{hdr|===}}} | ||
Use <code>--in</code> followed by your file name to specify the SAM/BAM input file. | Use <code>--in</code> followed by your file name to specify the SAM/BAM input file. | ||
Revision as of 17:36, 3 January 2014
input File (--in)
Use --in followed by your file name to specify the SAM/BAM input file.
The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
A - is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
| SAM/BAM/Uncompressed BAM from file | --in yourFileName
|
| SAM from stdin | --in -
|
| BAM from stdin | --in -.bam
|
| Uncompressed BAM from stdin | --in -.ubam
|
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the samtools implementation so pipes between our tools and samtools are supported.
