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{{{hdr|===}}} input File (<code>--in</code>) {{{hdr|===}}}
{{{hdr|===}}} Input File ({{#if: {{{noParam|}}} | {{{noParam}}} Parameter|<code>{{{param|--in}}}</code>}}) {{{hdr|===}}}
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.}}
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.
{|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>
|}
|}
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.
