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Issue #2905 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15342?detail_id=1611">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Closed</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>I'm going to make this as closed. The Python wrappers for the samtools later htslib C API do a fine job: pysam <a class="external" href="https://github.com/pysam-developers/pysam">https://github.com/pysam-developers/pysam</a></p>
<p>Thanks all.</p>
<p>Peter</p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2905#change-15342">Bug #2905: Short read alignment format SAM / BAM</a></h1>
<ul><li>Author: Osvaldo Zagordi</li>
<li>Status: Closed</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: Not Applicable</li>
<li>URL: </li></ul>
<p>Hi again,<br />is there any plan to develop some parsers for alignment of short reads? There's a lot of formats around, and the most serious proposal for a format I've seen is SAM (<a class="external" href="http://samtools.sourceforge.net/">http://samtools.sourceforge.net/</a>). I should start writing something to parse this output soon. Any suggestion on where to start from (in order not to depend on some module that will be soon obsolete)?</p>
<p>Thanks,<br /> Osvaldo</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1498/SamBamIO.py">SamBamIO.py</a>
(9.06 KB)<br />
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