Hello,<br><br>I am new at using the galaxy server and i have come across an annoying restriction when it comes to bam files.<br>There is an assumption build in, that a bam file needs to be coordinate sorted. (does hold for most tools). However, most of my tools are using the bam file coming off the mapper. (saves some time by not having to do sorting).<br>
Is there any way to get around this restriction? <br>Right now i&#39;ve hacked it to always return false for binary.py::dataset_content_needs_grooming.<br>I do however think that this could be a property of the bam file. A classification of the sort &quot;Unkown&quot;, &quot;Name Sorted&quot;, &quot;Position sorted&quot; sounds like a good idea to me.<br>
<br>Regards,<br>-Paul<br>