[mira_talk] Re: Duplicate contig name in maf to samnbb conversion
- From: Martin MOKREJŠ <mmokrejs@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 18 Jun 2014 09:35:59 +0200
Bastien Chevreux wrote:
> On 17 Jun 2014, at 23:12 , John Nash <john.he.nash@xxxxxxxxx> wrote:
>> If you want a samnbb outfile, do NOT add the .sam suffix. miraconvert uses
>> the outfile suffix to determine the desired outfile and the "-t samnbb"
>> switch and outfile.sam clash.
>
> D’oh, and I’ve started downloading your file just minutes ago :-)
>
> Anyway … that sounds as if I should rework the logic a bit. Indeed, in former
> times only “-t” was accepted, and even multiple of them were allowed (so
> multiple conversions could be made in one go). When I added the logic to
> parse out the desired formats from the file names (allowing e.g. “miraconvert
> fasta a.caf b.fastq”), I treat the format of the target file as additional
> “-t” option, allowing, e.g., “miraconvert -t fasta a.caf b.fastq” which will
> convert to fasta and fastq at the same time.
>
> However, SAMNOBB being rather an option of SAM and both having the same file
> ending, this seems to somehow confuse the existing logic. I need to fix that.
>
> Thanks for finding out.
Likewise, I have problems with "sff_extract -o" (seems like an output file, but
in real that is a prefix only). Using "-p" would have been much clearer.
M.
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