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