[miso-users] RuntimeWarning: Long inserted/deleted alignment

[Yarden Katz]

Hi Lee,

This is generally fine -- it means that you have alignments with cigar strings with insertions/deletions in their alignment.  These are ignored by MISO (i.e. indels not supported), but it still outputs the warning.  So it's okay to have these reads there, but they won't be used for inference, since they technically don't match the annotated isoforms. 

If you use an aligner that doesn't output indels, or if you turn indel alignment off, these should go away.

Best, --Yarden



On Apr 15, 2013, at 9:04 AM, Lee Sam wrote:

> I'm running some samples that I've aligned with GSNAP and I've got a lot 
> of the following messages:
> 
> "RuntimeWarning: Long inserted alignment at pysplicing/src/solve.c:262"
> "RuntimeWarning: Long deleted alignment at pysplicing/src/solve.c:262"
> 
> Is this something I should be concerned with?
> 
> Thanks,
> -Lee
> 
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