Difference between revisions of "Template:InBAMInputFile"

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{{{hdr|===}}} Input File ({{#if: {{{noParam|}}} | {{{noParam}}} Parameter|<code>{{{param|--in}}}</code>}}) {{{hdr|===}}}
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{{{hdr|===}}} Input File ({{#if: {{{noParam|}}} | {{{noParam}}} argument|<code>{{{param|--in}}}</code>}}) {{{hdr|===}}}
  
{{#if: {{{noParam|}}} | The {{{noParam}}} argument is the input SAM/BAM file. |
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{{#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.