Bowtie users: If you want bowtie in Jessie please answer this question (Was: Help for preparing bowtie upload)
Hi,
I really need the answer of a bowtie user to the question below whether
the test can be regarded successful or not. If not I'd hesitate to
upload which might mean that bowtie remains RC buggy and will not make
it into the next stable release.
Thanks
Andreas.
On Wed, Sep 03, 2014 at 12:27:35PM +0200, Andreas Tille wrote:
> Hi,
>
> as you might know bowtie fails to build on several architectures
> #756780. As I said in my previous mail to this list (and upstream) this
> is caused by using an outdated arch-specific copy of an internal gcc
> header file. To be sure that my fix really works I added a test suite
> which is oriented at the upstream manual and reproduces the output given
> there.
>
> This was possible with the exception of one example:
>
> $ bowtie -a --best -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
>
> is supposed to have the output
>
> - gi|110640213|ref|NC_008253.1| 2852852 8:T>A
> + 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| 148810 10:A>G,13:C>G
> - gi|110640213|ref|NC_008253.1| 4930433 4:G>T,6:C>G
>
> according to the manual but produces with the current arch-amd64
> specific build in unstable as well as with the new build
>
> - 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
>
> which has the only difference that the original line 4 went to line 2
> now (all output files and the diff attached).
>
> As a proof of my terribly poor knowledge in this field I wonder whether
> this is an issue or not. I guess I could simply use the current output
> as comparison template but I's like to hear some confirmation. If you
> confirm so I'd plan to upload and see what happens on all the other
> architectures.
>
> Kind regards and thanks for your insight
>
> Andreas.
>
> --
> http://fam-tille.de
> - gi|110640213|ref|NC_008253.1| 2852852 8:T>A
> + 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| 148810 10:A>G,13:C>G
> - gi|110640213|ref|NC_008253.1| 4930433 4:G>T,6:C>G
> - 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
> --- example5.out.orig 2014-09-03 11:27:25.000000000 +0200
> +++ example5.out 2014-09-03 12:16:13.612777963 +0200
> @@ -1,5 +1,5 @@
> - 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| 148810 10:A>G,13:C>G
> - gi|110640213|ref|NC_008253.1| 4930433 4:G>T,6:C>G
--
http://fam-tille.de
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