[mira_talk] Re: Duplicate contig name in maf to samnbb conversion
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 17 Jun 2014 23:25:56 +0200
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.
B.
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