[mira_talk] Re: Getting coverage by each technology per each contig
- From: Martin MOKREJŠ <mmokrejs@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 23 May 2014 14:31:18 +0200
Bastien Chevreux wrote:
> On 21 May 2014, at 21:07 , Martin MOKREJŠ <mmokrejs@xxxxxxxxx
> <mailto:mmokrejs@xxxxxxxxx>> wrote:
>> […]
>> Would *_contigstats.txt contain one more column with the sequencing
>> technology abbreviated, things
>> would have been even easier.
>
> I know. But then again some people would want to have it not by sequencing
> tech, but by readgroup … and the format of the contigstats would start to
> become fluid instead of fixed. Not good.
I had the same idea that some people will want to split by strain. It is
obvious goal.
But, I disagree that the format of contigstats should remain as it is. Parsing
a multi-column
file is trivial and those who need old number of columns, can throw some away
using awk.
Don't know how other but I find mira so much changing (evolving) tat I wouldn't
care about
an extra few columns in contigstats file.
>
> On the other hand: for things like this one should really parse the MAF file.
> It’s practically developed for easy processing :-)
Interestingly, I certainly wanted to avoid that. ;)
Martin
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