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470 bytes added
, 22:31, 8 April 2019
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− | {{{hdr|===}}} input File (<code>--in</code>) {{{hdr|===}}} | + | {{{hdr|===}}} Input File ({{#if: {{{noParam|}}} | {{{noParam}}} argument|<code>{{{param|--in}}}</code>}}) {{{hdr|===}}} |
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− | Use <code>--in</code> followed by your file name to specify the SAM/BAM input file. | + | {{#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.}} |
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− | 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.}} |
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− | 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|}}}|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).}} |
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| {|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>--in yourFileName</code> | + | | <code>{{#if: {{{noParam|}}} | |--in}} yourFileName</code> |
− | |- | + | {{#if: {{{noStdin|}}} | |<tr> |
− | |SAM from stdin
| + | <td>SAM from stdin</td> |
− | | <code>--in -</code>
| + | <td><code>{{#if: {{{noParam|}}} | |--in}} -</code></td></tr> |
− | |-
| + | <tr> |
− | |BAM from stdin
| + | <td>BAM from stdin</td> |
− | | <code>--in -.bam</code>
| + | <td><code>{{#if: {{{noParam|}}} | |--in}} -.bam</code></td></tr> |
− | |-
| + | <tr> |
− | |Uncompressed BAM from stdin
| + | <td>Uncompressed BAM from stdin</td> |
− | | <code>--in -.ubam</code>
| + | <td><code>{{#if: {{{noParam|}}} | |--in}} -.ubam</code></td></tr>}} |
| |} | | |} |
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| 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. |