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
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|{{#if: {{{noStdin|}}} | |SAM from stdin}}
 
| <code>{{#if: {{{noParam|}}} | |--in}} -</code>
 
| <code>{{#if: {{{noParam|}}} | |--in}} -</code>
 
|-
 
|-

Revision as of 21:17, 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.