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264 bytes added
, 16:49, 6 January 2014
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− | {{{hdr|===}}} input File (<code>--in</code>) {{{hdr|===}}} | + | {{{hdr|===}}} Input File ({{#if: {{{noParam|}}} | {{{noParam}}} Parameter|<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 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, unless your input file is stdin. |
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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> |
| |- | | |- |
| |SAM from stdin | | |SAM from stdin |
− | | <code>--in -</code> | + | | <code>{{#if: {{{noParam|}}} | |--in}} -</code> |
| |- | | |- |
| |BAM from stdin | | |BAM from stdin |
− | | <code>--in -.bam</code> | + | | <code>{{#if: {{{noParam|}}} | |--in}} -.bam</code> |
| |- | | |- |
| |Uncompressed BAM from stdin | | |Uncompressed BAM from stdin |
− | | <code>--in -.ubam</code> | + | | <code>{{#if: {{{noParam|}}} | |--in}} -.ubam</code> |
| |} | | |} |
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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. |