Re: RFS: bowtie/1.2.1.1+dfsg-1

[Andreas Tille <andreas@an3as.eu>]

Hi Alex,

thanks a lot for your work on this.  I'd consider this quite important
but I would prefer if someone more educated than I who knows what the
test issues might mean would have another look.  Please ping me again
if nobody would step in (should there really nobody interested???) and
I'll sponsor as is.

Thanks again

      Andreas.

On Thu, Oct 19, 2017 at 06:16:39PM +0200, Alex Mestiashvili wrote:
> Hello,
> 
> I've worked a bit on bowtie in git [0] and think that it is ready for
> upload. It also presumably closes #864439. One of the issues I run
> during package building is that bowtie unit tests fail on example6 and
> exmaple9.
> Could somebody who uses bowtie please comment on this ? Not sure if this
> is something I should report upstream.
> 
> bowtie -a --best --strata -v 2 --suppress 1,5,6,7 e_coli -c
> ATGCATCATGCGCCAT > example6.out
> 
> bowtie 1.1.2-6
> 
> cat example6.out
> -       gi|110640213|ref|NC_008253.1|   2852852 8:T>A
> 
> bowtie 1.2.1.1+dfsg-1
> 
> cat example6.out
> -       gi|110640213|ref|NC_008253.1|   2852852 8:T>A
> -       gi|110640213|ref|NC_008253.1|   148810  10:A>G,13:C>G
> +       gi|110640213|ref|NC_008253.1|   1093035 2:T>G,15:A>T
> -       gi|110640213|ref|NC_008253.1|   905664  6:A>G,7:G>T
> -       gi|110640213|ref|NC_008253.1|   4930433 4:G>T,6:C>G
> 
> bowtie -a -m 3 --best --strata -v 2 e_coli --suppress 1,5,6,7 -c
> ATGCATCATGCGCCAT      > example9.out
> 
> bowtie 1.1.2-6
> 
> cat example9.out
> -       gi|110640213|ref|NC_008253.1|   2852852 8:T>A
> 
> bowtie 1.2.1.1+dfsg-1
> 
> produces empty example9.out
> 
> Thank you,
> Alex
> 
> [0] https://anonscm.debian.org/git/debian-med/bowtie.git
> 
> 

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