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104 changes: 51 additions & 53 deletions convert-sam-for-rsem.html
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<head>
<title>convert-sam-for-rsem</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:root@localhost" />
<link rev="made" href="mailto:root@osx004.apple.com" />
</head>

<body style="background-color: white">


<!-- INDEX BEGIN -->
<div name="index">
<p><a name="__index__"></a></p>

<ul>

<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#arguments">ARGUMENTS</a></li>
<li><a href="#options">OPTIONS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<ul id="index">
<li><a href="#NAME">NAME</a></li>
<li><a href="#SYNOPSIS">SYNOPSIS</a></li>
<li><a href="#ARGUMENTS">ARGUMENTS</a></li>
<li><a href="#OPTIONS">OPTIONS</a></li>
<li><a href="#DESCRIPTION">DESCRIPTION</a></li>
<li><a href="#EXAMPLES">EXAMPLES</a></li>
</ul>

<hr name="index" />
</div>
<!-- INDEX END -->
<h1 id="NAME">NAME</h1>

<p>
</p>
<h1><a name="name">NAME</a></h1>
<p>convert-sam-for-rsem</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>

<h1 id="SYNOPSIS">SYNOPSIS</h1>

<p>convert-sam-for-rsem [options] &lt;input.sam/input.bam&gt; output_file_name</p>
<p>
</p>
<hr />
<h1><a name="arguments">ARGUMENTS</a></h1>

<h1 id="ARGUMENTS">ARGUMENTS</h1>

<dl>
<dt><strong><a name="input_sam_input_bam" class="item"><strong>input.sam/input.bam</strong></a></strong></dt>

<dt id="input.sam-input.bam"><b>input.sam/input.bam</b></dt>
<dd>
<p>The SAM or BAM file generated by user's aligner. We require this file contains the header section. If input is a SAM file, it must end with suffix 'sam' (case insensitive). If input is a BAM file, it must end with suffix 'bam' (case insensitive).</p>
</dd>
<dt><strong><a name="output_file_name" class="item"><strong>output_file_name</strong></a></strong></dt>

<p>The SAM or BAM file generated by user&#39;s aligner. We require this file contains the header section. If input is a SAM file, it must end with suffix &#39;sam&#39; (case insensitive). If input is a BAM file, it must end with suffix &#39;bam&#39; (case insensitive).</p>

</dd>
<dt id="output_file_name"><b>output_file_name</b></dt>
<dd>
<p>The output name for the converted file. 'convert-sam-for-rsem' will output a BAM with the name 'output_file_name.bam'.</p>

<p>The output name for the converted file. &#39;convert-sam-for-rsem&#39; will output a BAM with the name &#39;output_file_name.bam&#39;.</p>

</dd>
</dl>
<p>
</p>
<hr />
<h1><a name="options">OPTIONS</a></h1>

<h1 id="OPTIONS">OPTIONS</h1>

<dl>
<dt><strong><a name="t_temporary_directory_directory" class="item"><strong>-T/--temporary-directory</strong> &lt;directory&gt;</a></strong></dt>

<dt id="T---temporary-directory-directory"><b>-T/--temporary-directory</b> &lt;directory&gt;</dt>
<dd>
<p>'convert-sam-for-rsem' will call 'sort' command and this is the '-T/--temporary-directory' option of 'sort' command. The following is the description from 'sort' : &quot;use DIR for temporaries, not $TMPDIR or /tmp; multiple options specify multiple directories&quot;.</p>
</dd>
<dt><strong><a name="h_help" class="item"><strong>-h/--help</strong></a></strong></dt>

<p>&#39;convert-sam-for-rsem&#39; will call &#39;sort&#39; command and this is the &#39;-T/--temporary-directory&#39; option of &#39;sort&#39; command. The following is the description from &#39;sort&#39; : &quot;use DIR for temporaries, not $TMPDIR or /tmp; multiple options specify multiple directories&quot;.</p>

</dd>
<dt id="h---help"><b>-h/--help</b></dt>
<dd>

<p>Show help information.</p>

</dd>
</dl>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<p>This program converts the SAM/BAM file generated by user's aligner into a BAM file which RSEM can process. However, users should make sure their aligners use 'reference_name.idx.fa' generated by 'rsem-prepare-reference' as their references and output header sections. This program will create a temporary directory called 'output_file_name.bam.temp' to store the intermediate files. The directory will be deleted automatically after the conversion. After the conversion, this program will call 'rsem-sam-validator' to validate the resulting BAM file.</p>
<p>Note: You do not need to run this script if `rsem-sam-validator' reports that your SAM/BAM file is valid.</p>

<h1 id="DESCRIPTION">DESCRIPTION</h1>

<p>This program converts the SAM/BAM file generated by user&#39;s aligner into a BAM file which RSEM can process. However, users should make sure their aligners use &#39;reference_name.idx.fa&#39; generated by &#39;rsem-prepare-reference&#39; as their references and output header sections. This program will create a temporary directory called &#39;output_file_name.bam.temp&#39; to store the intermediate files. The directory will be deleted automatically after the conversion. After the conversion, this program will call &#39;rsem-sam-validator&#39; to validate the resulting BAM file.</p>

<p>Note: You do not need to run this script if `rsem-sam-validator&#39; reports that your SAM/BAM file is valid.</p>

<p>Note: This program does not check the correctness of input file. You should make sure the input is a valid SAM/BAM format file.</p>
<p>
</p>
<hr />
<h1><a name="examples">EXAMPLES</a></h1>
<p>Suppose input is set to 'input.sam' and output file name is &quot;output&quot;</p>
<pre>
convert-sam-for-rsem input.sam output</pre>
<p>We will get a file called 'output.bam' as output.</p>

<h1 id="EXAMPLES">EXAMPLES</h1>

<p>Suppose input is set to &#39;input.sam&#39; and output file name is &quot;output&quot;</p>

<pre><code> convert-sam-for-rsem input.sam output</code></pre>

<p>We will get a file called &#39;output.bam&#39; as output.</p>


</body>

</html>


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