Hi there,

I'm using [svtyper][1] in order to get the genotype of some structural variants called using `Lumpy`. Svtyper starts running and everything seems OK until it arrives to a specific variant of the input vcf file. At this record, svtyper crashes with the following error:

```
File "pysam/calignmentfile.pyx", line 836, in pysam.calignmentfile.AlignmentFile.mate (pysam/calignmentfile.c:10945)
ValueError: mate not found
```

svtyper calls pysam at some point to get the mate pairs. I've read the code of pysam, and this is what I've found:

    Throws a ValueError if read is unpaired or the mate is unmapped.

So, I think that svtyper crashes due to the presence of a read with unmapped mate supporting the SV. If this is the true reason of the error, does this make sense? I mean, I'm interested also in those reads which their mate is unmapped, this is a good pointer about the presence of a SV in that position, isn't it?

Any ideas?

 [1]: https://github.com/cc2qe/svtyper
<p>Well, I did not know where the problem comes from but I found a &quot;temporary&quot; solution just in case that anyone is struggling to get this.<br />
Using <code>samblaster</code> tool (available here:<a href="https://github.com/GregoryFaust/samblaster">https://github.com/GregoryFaust/samblaster</a>) with <code>--addMateTags</code>, mate tags (MC, MQ) are added to the bam file. Without them, <code>svtyper</code> must seek to the corresponding mate position in the bam file. Using this approach, <code>svtyper</code> and therefore <code>pysam</code>, works nice without any error, and also, faster.</p>
