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Move all NeXML related modules and tests to a new Bio-NeXMLIO distribution.
2018-09-10
C
a
rn
ë
D
raug
Move al
l
N
eXML related
m
o
dules and
test
s
t
o
a new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë
D
raug
Rem
o
ve some u
n
used test data files
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Draug
Remove entire
B
io::P
o
pGen nam
e
space and related modules
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
Carn
ë
Draug
scripts/tr
e
e/bp_blast2tree
.
pl
:
mov
e
d
to
b
ioperl-ru
n
commit
|
commitdiff
|
tree
2018-09-07
Carn
ë
Dr
a
ug
d
eobfusca
t
or:
remove this whole proj
e
ct
commit
|
commitdiff
|
tree
2018-09-04
Carnë
D
raug
Cons
i
stent
s
h
ebang line to '+#!/usr/bin/perl'
commit
|
commitdiff
|
tree
2018-08-23
Car
n
ë Draug
deobfuscator scri
p
ts: use
warnings pragma
instead of
.
.
.
commit
|
commitdiff
|
tree
2018-07-25
Car
n
ë
D
raug
B
io
:
:MolEvol::CodonModel:
f
i
x docu
m
entat
i
on (issue
.
.
.
commit
|
commitdiff
|
tree
2017-09-13
C
a
rnë Draug
examples/a
l
ign/cl
u
s
talw
.
pl: remove
f
ile, n
o
w part of
.
.
.
commit
|
commitdiff
|
tree
2017-09-08
Carnë Draug
Removal of Bio::
T
o
o
ls::Ph
y
lo::PAML
.
pm
a
nd rela
t
ed modules
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Carnë Draug
B
io::Ph
y
loNe
t
work::muVe
c
t
o
r: revert non-typ
o
from
5
4c99cf411
commit
|
commitdiff
|
tree
2017-08-30
Carnë
Draug
maint:
fix mu
l
t
iple typos identified by lintian
commit
|
commitdiff
|
tree
2015-11-29
Ca
r
n
ë
Draug
bp
_
pairwise_kaks
.
pl: d
o
n
ot mix space and tabs for
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carn
ë
D
ra
u
g
Bio::Align::
U
tilities - remove usag
e
of /r opti
o
n t
o
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Ca
r
në Draug
Fix non
s
ense in code comments
.
commit
|
commitdiff
|
tree
2013-11-26
Ca
r
në Dr
a
ug
Bio
:
:Align::Utilities - follow some p
e
r
l
best
practices
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
Bio::Al
i
g
n::Utilities - new func
t
io
n
most_com
m
on_sequen
c
es
commit
|
commitdiff
|
tree
2013-11-26
C
a
rnë Draug
Bio::SimpleAlign - fol
l
o
w some perl best practices
commit
|
commitdiff
|
tree
2013-04-04
Carnë Draug
maint: remov
e
files that have been
m
o
v
ed t
o
a se
p
a
rate
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Car
n
ë
Dra
u
g
maint: up
d
ate Changes after re
m
ov
i
ng f
i
le
s
f
r
om Bio
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Draug
maint: remove
f
i
l
e
s
that have
b
e
en move
d
to a
s
eparat
e
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
C
a
r
n
ë
Draug
tests: move tests from R
o
ot
to As
s
embly and SeqIO
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
ma
i
nt: remove hard t
a
bs and tr
a
iling w
h
itespace
commit
|
commitdiff
|
tree
2013-03-28
Carnë Dr
a
ug
t
e
sts f
o
r
inheritance should b
e
long on the ch
i
ld class
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
remove hard t
a
bs and
t
railing w
h
itespace from som
e
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Drau
g
Annotation:
f
ix typo on test
commit
|
commitdiff
|
tree
2013-03-26
Carnë
Draug
Bio::C
l
uster::
S
equenceFamily - bug fixes
and performanc
e
commit
|
commitdiff
|
tree
2013-03-26
Ca
r
në Draug
d
o
c: fix indentation,
remove hard tabs and
t
railing
.
.
.
commit
|
commitdiff
|
tree
2013-03-21
Car
n
ë
Draug
recover GenericWebAgent f
r
o
m Bio-
E
Utili
t
ies
commit
|
commitdiff
|
tree
2013-03-13
Carnë Dra
u
g
spl
i
t Bio
-
Biblio
into a s
e
parate distribution
commit
|
commitdiff
|
tree
2013-03-12
Carnë
Draug
Merg
e
pull request #53
f
rom bvaisvil
/
m
aster
commit
|
commitdiff
|
tree
2013-03-06
Carnë Draug
Bio::Perl -
f
ix in
d
e
ntation (remove tabs,
a
nd w
e
ird
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Car
n
ë Draug
D
o
n't use a separate default scalar when there's a
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Car
n
ë Draug
fo
l
lo
w
p
e
rl
r
ecommendations:
commit
|
commitdiff
|
tree
2013-03-04
Carnë Draug
fix i
n
dentation
(remo
v
e
tabs, and wei
r
d
3 spa
c
es indentation)
commit
|
commitdiff
|
tree
2013-03-04
Carnë Dra
u
g
follow
p
e
r
l reco
m
mendations:
commit
|
commitdiff
|
tree
2013-03-04
Carnë Draug
use unti
l
instead o
f
w
hi
l
e
(
1
){las
t
i
f
.
.
.
}
commit
|
commitdiff
|
tree
2013-03-04
Ca
r
në Draug
f
ix indentat
i
on
(remove tabs, 3 space
a
n
d
2
s
pace i
n
dent
a
tion)
commit
|
commitdiff
|
tree
2013-02-11
Car
n
ë Draug
removing
B
i
o
:
:Feat
u
reI
O
and Bio::SeqFeature::Annotated
.
.
.
commit
|
commitdiff
|
tree
2013-02-06
Ca
r
në Draug
main
t
: ment
i
o
n
r
ece
n
t changes
to Bio::Seq
I
O::f
a
sta
commit
|
commitdiff
|
tree
2013-02-06
Carnë Draug
Bi
o
::SeqIO::fasta - rem
o
ve
package
v
ariables
for defaults
commit
|
commitdiff
|
tree
2013-02-05
Ca
r
në D
r
aug
Bio::SeqIO::fasta - implement
block
m
etho
d
for pretty
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Ca
r
në Drau
g
f
ollow perl recommendations:
commit
|
commitdiff
|
tree
2013-01-28
C
arnë Dr
a
ug
finish mov
i
ng the Bio-D
B
-EUtilitie
s
to
t
he Bio-EUtilities
.
.
.
commit
|
commitdiff
|
tree
2013-01-28
Carnë Draug
Fixi
n
g POD documenta
t
i
on
.
Empty line before
=
cut
t
o
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carnë Dr
a
ug
genbank
_
ref_extr
a
ctor: mov
e
'require'
s
to
GetOptions
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carnë Drau
g
genbank_re
f
_
e
x
tractor: cha
n
g
e
d
default assembly
r
egex
commit
|
commitdiff
|
tree
2011-09-28
Carnë Draug
genbank_ref_e
x
tra
c
tor: s
m
al
l
typo on docum
e
nt
a
t
ion
commit
|
commitdiff
|
tree
2011-09-28
C
a
rnë
D
raug
genbank_r
e
f_extr
a
ctor: added assembly to
e
x
ported dat
a
commit
|
commitdiff
|
tree
2011-09-22
Carnë D
r
aug
genbank_re
f
_extracto
r
: typo on al
l
instances of v
a
r
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
Carnë Draug
genban
k
_re
f
_ex
t
ra
c
tor: small fixes on P
O
D documentation
commit
|
commitdiff
|
tree
2011-09-21
C
arnë Draug
g
e
nbank_r
e
f_extract
o
r
:
new s
c
ript to make sear
c
h on
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
C
a
r
n
ë
Dr
a
ug
Fix bug when u
s
ing S
T
DOUT or writing to file
wit
h
out
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
Imp
r
ove
m
ents t
o
POD
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
replaced identation tabs fo
r
s
p
a
ces
commit
|
commitdiff
|
tree
2011-07-25
Carnë Draug
Don'
t
m
e
ss with
$^W
.
Control with
w
a
rni
n
gs
p
ragm
a
instead
commit
|
commitdiff
|
tree
2011-07-25
C
arnë Dr
a
ug
scri
p
ts: added 'us
e
warnings' to a
l
l
s
crip
t
s without
it
commit
|
commitdiff
|
tree
2011-07-25
Carnë Dr
a
ug
scripts: re
p
lace
d
-w switch by use w
a
rni
n
gs
commit
|
commitdiff
|
tree
2011-07-20
C
arnë Draug
Scr
i
pt do
c
umentation fix to match their names
w
ith
.
.
.
commit
|
commitdiff
|
tree
2011-07-19
Carnë Draug
R
e
named al
l
scri
p
t
s with
p
rfix bp
_
commit
|
commitdiff
|
tree