[Debian-med-packaging] RFS: bowtie/1.2.1.1+dfsg-1

[Alex Mestiashvili]

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