Difference between revisions of "Template:InBAMInputFile"
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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.}} | 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.}} | ||
| − | {{#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).}} | + | {{#if: {{{noStdin|}}}|Note: 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" | ||
Latest revision as of 22:31, 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.
