Template:InBAMInputFile: Difference between revisions
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{{{hdr|===}}} Input File ({{#if: {{{noParam|}}} | {{{noParam}}} | {{{hdr|===}}} Input File ({{#if: {{{noParam|}}} | {{{noParam}}} argument|<code>{{{param|--in}}}</code>}}) {{{hdr|===}}} | ||
{{#if: {{{noParam|}}} | The {{{noParam}}} argument is the input SAM/BAM file. | | {{#if: {{{noParam|}}} | The {{{noParam}}} argument is the name of the input SAM/BAM file. | | ||
Use <code>{{{param|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}} | Use <code>{{{param|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}} | ||
Revision as of 16:53, 6 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.
