[mira_talk] Re: Parse error at line 84: unmatched CIGAR operation
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 28 Mar 2013 19:07:56 +0000
On Wed, Mar 27, 2013 at 9:11 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
> On Wednesday, March 27, 2013, John Nash wrote:
>>
>> >> B. Peter Cock's maf2sam.py (version 2.0) hangs when I try to convert
>> >> the maf file to a sam file.
>> >
>> > I never updated it to cope with the MAF from MIRA v3.9.x, but
>> > if you fancy sharing the data I can have a look at make it at least
>> > give a clear error. There seemed little point as MIRA v3.9.x has
>> > native SAM output.
>>
>> Fair enough, I was grasping at straws by then. I don't want to give you
>> extra work but if you would be kind enough to look at a 330 megabyte gzipped
>> maf file, I can send you the link backchannel as soon as it uploads to
>> Dropbox.
>
> If you're uploading it to Dropbox anyway, I'll try and find a moment
> to look at it later this week/weekend.
I've got John's example MAF file now, and from my initial exploration
I think I'll be able to update maf2sam.py to cope with this too. That
would then be quite useful for debugging the CIGAR issue that
samtools complains about, and confirm where this comes from.
(John - can you keep the file on Dropbox a bit longer in case we
need Bastien to look at it for the MIRA convert_project handling)
Regards,
Peter
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
