Template:InBAMInputFile: Difference between revisions
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{{{hdr|===}}} | {{{hdr|===}}} Input File ({{#if: {{{noParam|}}} | {{{noParam}}} Parameter|<code>{{{param|--in}}}</code>}}) {{{hdr|===}}} | ||
Use <code>--in</code> followed by your file name to specify the SAM/BAM input file. | {{#if: {{{noParam|}}} | The {{{noParam}}} argument is the input SAM/BAM 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, unless your input file is stdin. | ||
| Line 9: | Line 10: | ||
{|border="1" cellspacing="0" cellpadding="2" | {|border="1" cellspacing="0" cellpadding="2" | ||
|SAM/BAM/Uncompressed BAM from file | |SAM/BAM/Uncompressed BAM from file | ||
| <code>--in yourFileName</code> | | <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code> | ||
|- | |- | ||
|SAM from stdin | |SAM from stdin | ||
| <code>--in -</code> | | <code>{{#if: {{{noParam|}}} | |--in}} -</code> | ||
|- | |- | ||
|BAM from stdin | |BAM from stdin | ||
| <code>--in -.bam</code> | | <code>{{#if: {{{noParam|}}} | |--in}} -.bam</code> | ||
|- | |- | ||
|Uncompressed BAM from stdin | |Uncompressed BAM from stdin | ||
| <code>--in -.ubam</code> | | <code>{{#if: {{{noParam|}}} | |--in}} -.ubam</code> | ||
|} | |} | ||
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported. | Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported. | ||
Revision as of 16:49, 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.
