Difference between revisions of "Template:InBAMInputFile"
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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.}} | ||
| − | 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. | + | The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin|.}}}|, unless your input file is stdin.}} |
| − | A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM). | + | {{#if: {{{noStdin|This tool does not support input from stdin.}}}|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}} |
{|border="1" cellspacing="0" cellpadding="2" | {|border="1" cellspacing="0" cellpadding="2" | ||
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| <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code> | | <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code> | ||
|- | |- | ||
| − | |SAM from stdin | + | |{{#if: {{{noStdin|}}} | |SAM from stdin}} |
| <code>{{#if: {{{noParam|}}} | |--in}} -</code> | | <code>{{#if: {{{noParam|}}} | |--in}} -</code> | ||
|- | |- | ||
Revision as of 22:17, 8 April 2019
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.
