Difference between revisions of "Template:InBAMInputFile"

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{{{hdr|==}}} input File (<code>--in</code>) {{{hdr|==}}}
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{{{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.