[mira_talk] Re: Question: padded or unpadded outputs
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 24 Mar 2015 17:13:38 +0000
On Tue, Mar 24, 2015 at 9:52 AM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
> On Mon, Mar 23, 2015 at 10:55 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>> On 23 Mar 2015, at 23:18 , Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
>>> I think my script is getting confused by the * (gap)
>>> within the soft-clipped part of the read. I am guessing
>>> that MIRA did some trimming after some alignment
>>> process had inserted the gap.
>>
>> In a de-novo context this should never happen (at least I think
>> it should not). However, in a mapping context, this is likely to
>> happen when the option to trim overhanging reads is on (which
>> is default). As the trimming occurs only after all reads have been
>> aligned, one can get gaps in clipped parts of a reads which are
>> extending a given reference.
>
> I think Lenis was using MIRA in mapping mode, so that makes
> sense. This should be easy to deal with now I am aware that
> it can happen - the assert statement did its job and found an
> assumption I'd made didn't always hold :)
maf2sam.py v0.3.3 should handle this special case properly now:
https://github.com/peterjc/maf2sam/commit/eda9febf3bc7289e5b242d80ed999f1b3a8ec727
Thanks again Lenis for the test data file.
Peter
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