Help for preparing bowtie upload
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is caused by using an outdated arch-specific copy of an internal gcc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
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