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t/AlignIO/AlignIO.t: fix number of tests in plan (fixup c523e6bed866)
2018-09-17
Carnë
D
ra
u
g
t/Ali
g
n
I
O/Al
i
g
n
IO
.
t: fix number of test
s
in
p
lan (fixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Ca
r
në Draug
t/Annotation/Annota
t
ion
.
t: remove te
s
t for B
i
o
:
:SeqFe
a
ture
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio/
T
ools/Run/Phylo/PhyloBas
e
.
pm: bring
b
as
e
clas
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Draug
Bio/
T
ools/Phylo/Gumby
.
pm: move to its own distribu
t
io
n
commit
|
commitdiff
|
tree
2018-09-17
Ca
r
në Draug
DB/Seq
F
eature/Store/berke
l
eydb3
.
pm: f
i
x
errors so it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Drau
g
A
d
j
ust tes
t
s indirectly
maki
n
g
u
s
e
of Bio::AlignIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
bp_pro
c
ess_wormbase:
move progra
m
to new Bio-DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
bp_
n
etin
s
tall: remove ou
t
of date program
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
aug
Move modules dependent
o
n
Bio::Ext::Align into defunct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
B
i
o::DB
:
:Expression: move to defunct bioperl-
m
i
c
roarra
y
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint
:
644
p
ermis
s
io
n
s f
o
r
almost
a
ll files
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint: set all source code wi
t
h
u
t
f-8 encoding
commit
|
commitdiff
|
tree
2018-09-16
Carnë Dra
u
g
main
t
:
remove m
a
int
a
iner out of date fi
l
es
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
ide:
r
e
move module te
m
plat
e
s -
n
o longer needed after
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Ca
r
në Draug
ide/biop
e
rl-mode: int
o
its ow
n
rep
o
sitory to be developed
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
mai
n
t:
remove bi
o
per
l
-mode rel
e
ase tarball
s
f
rom ve
r
sion
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
Bio:
:
Index::Abs
t
r
a
c
t
->_type_
a
nd_ve
r
sion: check type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Car
n
ë
Draug
t/
L
o
c
alDB/
I
ndex/BlastTable
.
t
:
use
temp
d
ir to avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t/LocalDB/I
n
dex
/
Bl
a
st
.
t:
c
reate
test tempfi
l
es
within
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
arnë Draug
m
a
int: remove unused test d
a
t
a
f
i
l
e
s
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
Remov
e
Al
i
gnIO and Index sto
c
kholm
m
o
d
u
l
es to new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Carnë Dra
u
g
Bio:
:
DB::Univers
a
l: move i
n
t
o its
o
wn di
s
tri
b
ution
commit
|
commitdiff
|
tree
2018-09-14
C
arnë Drau
g
main
t
: sim
p
lify R
E
A
D
M
E t
o
c
over simple i
n
stall in
s
tru
c
ti
o
ns
.
commit
|
commitdiff
|
tree
2018-09-13
Carn
ë
Dr
a
ug
Bring
b
a
s
e classes from
BioPerl-run b
a
ck to BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
D
raug
Remove
use of Bio::Perl w
h
ich
h
a
s be
e
n moved to Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Bio::DB::MeSH mo
v
e to i
t
s ow
n
distrib
u
tion
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
Draug
Mo
v
e HMMER related modules, tests, and pr
o
gra
m
s to
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Bio::DB::TF
B
S name
s
pace has been
m
oved to i
t
s
own dist
r
i
buti
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
C
arnë Draug
Bio::D
B
::HIV and rela
t
ed
module
s
and scripts
moved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë
Draug
Bio::Al
i
gn::Gr
a
p
hics: m
o
ve into
its own distr
i
bution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carn
ë
Draug
Bio::To
o
ls::Run::RemoteBlast: mov
e
into a new di
s
tribut
i
on
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
a
rnë Draug
Bi
o
::Perl: move its own
d
i
s
tributio
n
named Bio-Proce
d
ural
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bio::Mol
E
vol::
C
odonM
o
d
el: move
i
nto
it separa
t
e
rep
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë
Draug
Bio
:
:Se
q
I
O::entrezgene: mo
v
e to existing B
i
o-ASN1
-
entrezgene
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
r
në
D
raug
Bio/Restriction/*: m
o
v
e
t
o anothe
r
repo with
same n
a
m
e
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
B
io/
T
o
o
ls/Gel
.
pm
:
move to
a
no
t
her
r
e
po with same name
.
commit
|
commitdiff
|
tree
2018-09-11
C
a
rn
ë
Draug
Bio/SeqEvolution/*: move to
a
n
other rep
o
wit
h
same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carn
ë
Draug
B
i
o
/
Str
u
cture/*: move to another repo with sam
e
name
.
commit
|
commitdiff
|
tree
2018-09-11
Car
n
ë Draug
t/data: remove more tes
t
data
f
il
e
s wh
i
c
h
moved to
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë
Draug
Bio/Assembly
*
:
move to
ano
t
h
er re
p
o
with
s
ame nam
e
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Dr
a
ug
B
io/PhyloN
e
tw
o
rk
*
: move to another
r
epo w
i
th
s
ame na
m
e
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Draug
Bio/SeqIO/excel
.
pm: mov
e
to another repo with same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë
Draug
Bi
o
/TreeIO
/
s
vggraph
.
pm: move t
o
another
repo with s
a
me
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Ca
r
në Draug
Bio
/
Tree
/
D
r
aw/Cladogram
.
pm: move to another repo with
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë D
r
aug
Bio
/
D
r
a
w
/Picto
g
ram
.
pm
:
move to another repo
w
ith
s
ame
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
C
a
rnë
D
ra
u
g
Mo
v
e
all modules interf
a
cing to ACeDB servers to a
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Ca
r
n
ë
Dra
u
g
M
ove all
NeXML r
e
lated mo
d
u
les and t
e
st
s
to a
n
ew Bi
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë
Dr
a
u
g
Re
m
ove
some unused test dat
a
files
.
commit
|
commitdiff
|
tree
2018-09-10
Carnë Drau
g
Remove entire Bio::P
o
pGen namespa
c
e an
d
r
elated modules
.
.
.
commit
|
commitdiff
|
tree
2018-09-08
Carnë Draug
scri
p
ts/t
r
ee
/
bp_bl
a
s
t2tree
.
pl: moved to bioperl-run
commit
|
commitdiff
|
tree
2018-09-07
Carnë Draug
deobf
u
scator
:
r
emove this wh
o
l
e
project
commit
|
commitdiff
|
tree
2018-09-04
Carnë Draug
C
o
n
sis
t
ent she
b
ang
lin
e
to '+
#
!/usr/bin/pe
r
l'
commit
|
commitdiff
|
tree
2018-08-23
Carnë Draug
deobfus
c
ator script
s
:
use w
a
rnings pr
a
g
m
a instea
d
of
.
.
.
commit
|
commitdiff
|
tree
2018-07-25
Ca
r
në D
r
aug
Bio::MolEvo
l
::Codon
M
odel: fix doc
u
menta
t
ion (issue
.
.
.
commit
|
commitdiff
|
tree
2017-09-13
C
a
rnë
Dra
u
g
examples/ali
g
n
/
clustalw
.
pl: remove file, now par
t
o
f
.
.
.
commit
|
commitdiff
|
tree
2017-09-08
Car
n
ë Draug
Removal of B
i
o::Tools::Phylo::PAM
L
.
p
m
a
n
d
related
m
odule
s
.
.
.
commit
|
commitdiff
|
tree
2017-08-31
Ca
r
në Draug
Bi
o
::PhyloNetwo
r
k::muVector:
revert non-typo fro
m
54c99cf411
commit
|
commitdiff
|
tree
2017-08-30
C
arnë D
r
aug
main
t
: fix m
u
ltipl
e
typos identified b
y
lintian
commit
|
commitdiff
|
tree
2015-11-29
Ca
r
n
ë
Drau
g
bp
_
pairw
i
s
e
_kaks
.
pl: do no
t
m
i
x space and
tabs for
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë Draug
B
i
o::Ali
g
n:
:
Util
i
ties
- remo
v
e usage of /r option to
.
.
.
commit
|
commitdiff
|
tree
2013-11-26
Carn
ë
D
r
aug
Fix nonsense in co
d
e comments
.
commit
|
commitdiff
|
tree
2013-11-26
Carnë D
r
a
u
g
Bio::Align::Utili
t
ies - fol
l
o
w
s
ome perl best pract
i
ces
.
commit
|
commitdiff
|
tree
2013-11-26
Ca
r
në Dr
a
ug
Bio::Al
i
gn::Utilities - new function most_common
_
sequ
e
nces
commit
|
commitdiff
|
tree
2013-11-26
C
a
rnë
Draug
B
io::SimpleAlign - follow so
m
e pe
r
l
bes
t
pr
a
ct
i
c
e
s
commit
|
commitdiff
|
tree
2013-04-04
C
a
rnë Draug
m
aint: r
e
move
f
iles th
a
t have
b
een moved to a separa
t
e
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë D
r
a
ug
maint: updat
e
Changes aft
e
r remov
i
ng
f
il
e
s from Bio
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
Carnë Dr
a
ug
maint:
r
emove files that have been move
d
to
a sep
a
ra
t
e
.
.
.
commit
|
commitdiff
|
tree
2013-04-02
C
ar
n
ë
Dra
u
g
tests:
m
ove t
e
sts fr
o
m
R
oot to Assembly a
n
d Seq
I
O
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë
Draug
maint: remove hard tabs and trailing wh
i
tespace
commit
|
commitdiff
|
tree
2013-03-28
Carnë Dra
u
g
t
ests for inher
i
tance s
h
ould belo
n
g on the child
clas
s
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carn
ë
Drau
g
remove hard tabs
a
nd trailing whitespac
e
from
some
.
.
.
commit
|
commitdiff
|
tree
2013-03-28
Carnë Draug
A
n
n
otation: fix
t
ypo on test
commit
|
commitdiff
|
tree
2013-03-26
Carnë
D
r
aug
Bio::Clust
e
r::Sequ
e
nceFamily - bug fixe
s
and performan
c
e
commit
|
commitdiff
|
tree
2013-03-26
Carnë Draug
doc: fix indent
a
tio
n
, remove
h
a
rd t
a
bs
a
n
d traili
n
g
.
.
.
commit
|
commitdiff
|
tree
2013-03-21
Carnë Draug
recover GenericWebAgent from Bi
o
-EUtiliti
e
s
commit
|
commitdiff
|
tree
2013-03-13
Ca
r
në Draug
split Bio
-
Bibl
i
o into a sepa
r
ate distribut
i
on
commit
|
commitdiff
|
tree
2013-03-12
Carnë Draug
Mer
g
e pull request
#53 from bvaisvi
l
/
master
commit
|
commitdiff
|
tree
2013-03-06
Car
n
ë Draug
Bio::Perl -
fix
indentation (remove tabs, and
wei
r
d
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Carnë
D
raug
D
o
n't
use
a
s
eparate default scalar when there's a
.
.
.
commit
|
commitdiff
|
tree
2013-03-04
Ca
r
në Draug
follow perl
recommenda
t
i
o
ns:
commit
|
commitdiff
|
tree
2013-03-04
Carn
ë
Draug
fix indentation (remove
t
abs, and weir
d
3 s
p
aces indentation
)
commit
|
commitdiff
|
tree
2013-03-04
Carnë Draug
foll
o
w pe
r
l recommendations:
commit
|
commitdiff
|
tree
2013-03-04
Car
n
ë Draug
use until ins
t
ead of wh
i
le(1){last if
.
.
.
}
commit
|
commitdiff
|
tree
2013-03-04
Car
n
ë Draug
fix inden
t
ation (remove tab
s
,
3 space a
n
d 2 space inde
n
tati
o
n)
commit
|
commitdiff
|
tree
2013-02-11
Carnë D
r
aug
r
e
movin
g
B
i
o::Featu
r
eIO a
n
d
Bio
:
:SeqFeatur
e
::An
n
otated
.
.
.
commit
|
commitdiff
|
tree
2013-02-06
Carnë D
r
aug
maint: mention recent changes t
o
Bio:
:
S
eqIO::f
a
sta
commit
|
commitdiff
|
tree
2013-02-06
Carnë Draug
Bio::SeqIO::fasta - remove package
variables for def
a
ults
commit
|
commitdiff
|
tree
2013-02-05
Carnë Draug
Bio:
:
Seq
I
O:
:
f
asta - implement block met
h
o
d
for pretty
.
.
.
commit
|
commitdiff
|
tree
2013-02-05
Ca
r
në Draug
follo
w
p
e
rl
recommendations:
commit
|
commitdiff
|
tree
2013-01-28
Carnë
Draug
fini
s
h
m
ovin
g
the Bio-DB-EUt
i
litie
s
to the Bio-E
U
tilities
.
.
.
commit
|
commitdiff
|
tree
2013-01-28
Carnë Draug
F
i
xing
P
O
D documentation
.
Empty line b
e
f
o
re =c
u
t to
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carnë Draug
g
e
n
bank_ref_extractor:
m
ove 'requi
r
e's to
G
etOptio
n
s
.
.
.
commit
|
commitdiff
|
tree
2011-09-28
Carnë Draug
gen
b
ank_ref_e
x
tractor: chang
e
d de
f
a
ult asse
m
bly regex
commit
|
commitdiff
|
tree
2011-09-28
C
a
rnë Draug
genbank_re
f
_extra
c
tor: sm
a
ll typo on documentation
commit
|
commitdiff
|
tree
2011-09-28
Carnë
D
raug
genbank_re
f
_extract
o
r:
added ass
e
mbly to expor
t
ed data
commit
|
commitdiff
|
tree
2011-09-22
C
a
rnë Draug
genbank_ref
_
extr
a
c
t
or: ty
p
o
on all instances
of var
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
Carnë Draug
g
e
nbank
_
ref_extractor
:
s
m
all fixes on POD d
o
c
u
ment
a
tion
commit
|
commitdiff
|
tree
2011-09-21
Carnë Drau
g
genbank_ref_extractor
:
new script to m
a
ke
s
earch
o
n
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
C
a
r
në
D
rau
g
F
i
x bug w
h
en us
i
ng STDOUT or wr
i
ting to file without
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
C
a
rn
ë
Draug
I
mprovemen
t
s to POD
commit
|
commitdiff
|
tree
next