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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{{#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).}}
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{{#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"
 
|SAM/BAM/Uncompressed BAM from file
 
|SAM/BAM/Uncompressed BAM from file
 
| <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code>
 
| <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code>
|-
+
{{#if: {{{noStdin|}}} | |<tr>
|{{#if: {{{noStdin|}}} | |SAM from stdin}}
+
<td>SAM from stdin</td>
| <code>{{#if: {{{noParam|}}} | |--in}} -</code>
+
<td><code>{{#if: {{{noParam|}}} | |--in}} -</code></td></tr>
|-
+
<tr>
|BAM from stdin
+
<td>BAM from stdin</td>
| <code>{{#if: {{{noParam|}}} | |--in}} -.bam</code>
+
<td><code>{{#if: {{{noParam|}}} | |--in}} -.bam</code></td></tr>
|-
+
<tr>
|Uncompressed BAM from stdin
+
<td>Uncompressed BAM from stdin</td>
| <code>{{#if: {{{noParam|}}} | |--in}} -.ubam</code>
+
<td><code>{{#if: {{{noParam|}}} | |--in}} -.ubam</code></td></tr>}}
 
|}
 
|}
  
  
 
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.

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.