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Bio::Tools::CodonTable and Bio::Tools::IUPAC: use our and drop BEGIN blocks.
2019-09-14
Carnë Draug
HA
C
KING
.
md: docu
m
ent th
a
t some documented names
p
aces
.
.
.
commit
|
commitdiff
|
tree
2019-08-29
Car
n
ë Draug
bp
_
cha
o
s_plot: remo
v
e scrip
t
(issue #32
3
)
commit
|
commitdiff
|
tree
2019-08-28
Ca
r
n
ë D
r
aug
v1
.
7
.
6
commit
|
commitdiff
|
tree
2019-08-28
Carnë Draug
m
a
i
nt upda
t
e Changes file
commit
|
commitdiff
|
tree
2019-06-07
Carnë Draug
dist
.
ini: list GD pr
e
req as suggestio
n
ins
t
ead of requiremen
.
.
.
commit
|
commitdiff
|
tree
2019-05-12
Ca
r
në Draug
bp_classif
y
_hit
s
_k
i
n
gdom:
move
from bin into examples
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
C
a
rnë Dr
a
ug
v1
.
7
.
5
commit
|
commitdiff
|
tree
2019-02-11
Car
n
ë Draug
Add
e
mpt
y
line aft
e
r
package statement
f
or $VERSION
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
SeqUtils
.
t: avoi
d
deprecated usage of
add_SeqFeature
commit
|
commitdiff
|
tree
2019-02-11
Carn
ë
Drau
g
ma
i
nt: mention
r
emoved methods
in
2
c
b
e4591d572
o
n Chang
e
s
.
.
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë
Draug
Bio::Seq::SeqW
i
thQuality
:
remove dep
r
eca
t
ed
class
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
Use /usr/bin/pe
r
l
i
n
stead
o
f env even
on exa
m
p
l
es
commit
|
commitdiff
|
tree
2019-02-11
Carnë
D
r
a
u
g
doc: fi
x
P
O
D in Bio::SeqIO::bsml so that
m
an can
ha
n
dle i
t
.
commit
|
commitdiff
|
tree
2019-02-11
Car
n
ë D
r
aug
lib/Bio/Tools/Run/README:
r
emove
file
commit
|
commitdiff
|
tree
2019-02-11
Carnë Dr
a
u
g
doc: add
NA
M
E sec
t
i
on with abstract to a
l
l mod
u
les
P
OD
commit
|
commitdiff
|
tree
2019-02-08
Carnë
D
raug
Bio
:
:Symbol:
mo
v
e to i
t
s own
distr
i
bution
commit
|
commitdiff
|
tree
2019-02-08
Carnë D
r
aug
do
c
: fix typ
o
s on doc foun
d
by Debian's lintian
commit
|
commitdiff
|
tree
2019-02-07
Carnë Draug
Bio::Root::Roo
t
I-
>
d
e
precated: fix when no version argume
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-02-07
Carnë
D
r
aug
Bio::Ro
o
t::R
o
otI: deprec
a
te
d
eprecated()
met
h
od (issu
e
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Carnë
Drau
g
v
1
.
7
.
4
commit
|
commitdiff
|
tree
2019-02-05
Carnë
Draug
maint: d
o
no
t
include travis configura
t
ion o
n
rele
a
se
commit
|
commitdiff
|
tree
2019-02-05
Carnë Dra
u
g
m
a
int: up
d
ate Cha
n
g
e
s f
o
r
u
pcomin
g
re
l
e
a
s
e
commit
|
commitdiff
|
tree
2019-02-05
Carnë Draug
t/SeqFeature/Gener
i
c
.
t: fix
typ
o
on required module
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Carnë Dra
u
g
Bio::Root::Test
:
fix
t
est_network use of
Test
:
:Requi
r
esI
n
ternet
commit
|
commitdiff
|
tree
2019-02-05
Carnë
Draug
maint: fix repo
s
itor
y
l
in
k
s on m
e
ta
d
ata (issue #3
0
6)
commit
|
commitdiff
|
tree
2019-01-30
Carnë Draug
v
1
.
7
.
3
commit
|
commitdiff
|
tree
2019-01-29
Carnë Draug
bi
n
/bp_genbank2gff3: fix
so
r
ting
b
y feature
type (issue
.
.
.
commit
|
commitdiff
|
tree
2019-01-29
Carnë Draug
Bio:
:
SeqIO::laser
g
ene: move to its
ow
n
distributi
o
n
commit
|
commitdiff
|
tree
2018-10-03
Carnë Draug
C
h
anges: more details and
philosophy a
r
e
o
n HACKING
.
.
.
commit
|
commitdiff
|
tree
2018-10-03
Carnë
D
raug
Changes: mor
e
d
e
tailed comp
l
et
e
list of
modules
/
d
ependencies
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë Drau
g
lib/Bi
o
P
e
rl
.
p
m: st
a
rt
conversio
n
of PO
D
t
o make use
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë D
r
aug
bi
n
/bp_biofetch_ge
n
bank_proxy: move
t
o Bio-D
B
-NCBIH
e
lper
commit
|
commitdiff
|
tree
2018-10-01
C
a
rnë
D
raug
B
io::DB::
S
wissProt: mo
v
e to
i
ts own di
s
tribution
commit
|
commitdiff
|
tree
2018-10-01
Car
n
ë Draug
Bio::
D
B::BioFetch: move to
i
t
s
ow
n
distri
b
u
t
ion
commit
|
commitdiff
|
tree
2018-09-30
C
a
rnë Draug
A
u
t
omati
c
ha
n
dling o
f
VERSION in al
l
modules (issue
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
t
/
SeqFeatur
e
/G
e
n
e
r
i
c
.
t:
f
ix
failing tests (fixup fde603f
2
2aa)
commit
|
commitdiff
|
tree
2018-09-30
C
a
r
në Draug
bin/bp_fetch
:
move require of optional modules
where
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
a
rnë Dra
u
g
Bio::M
a
p::
*
and Bio::MapI
O
::* : move i
n
to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
arnë Draug
Remo
v
e manipula
t
i
o
n
o
f
@
I
NC and use of lib - requir
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Dra
u
g
dist
.
ini: make Win
3
2 a dependency for Wind
o
ws only
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
arnë
D
rau
g
B
io::SeqIO
:
:agave: move to its
o
wn distribution
commit
|
commitdiff
|
tree
2018-09-29
Ca
r
në Draug
Bio
:
:SeqIO::chadoxml (and f
l
y
b
a
se_
c
hadoxml):
move t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
C
a
rnë Dra
u
g
maint: list Dat
a
::St
a
g::
X
MLWriter as dr
o
p
p
ed depende
n
cy
commit
|
commitdiff
|
tree
2018-09-29
Car
n
ë Draug
Bio::SeqIO::chaosxml (an
d
chaos
)
: mo
v
e to
th
e
ir o
w
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Dr
a
ug
Bio::Se
q
IO::strider: move into its
own di
s
tribution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dr
a
ug
Bio
:
:
T
ools::Protp
a
ram: move to its
ow
n
distrib
u
tion
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
maint:
upd
a
te and cle
a
n removed modules and de
p
e
n
d
e
nci
e
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Draug
B
i
o::DB::SeqVe
r
s
i
on: mo
v
e into its own distribution
commit
|
commitdiff
|
tree
2018-09-28
C
arnë Draug
Bio::Tools:
:
SiRNA and
r
e
l
ated
m
ove
d
to separ
a
te distr
i
bution
commit
|
commitdiff
|
tree
2018-09-28
Carnë
Draug
Bio::Too
l
s::Analysis::Pro
t
ein
:
move
modules into
t
heir
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::
T
o
ols::Analysis
:
:Pro
t
ein::Scansite
:
move to s
e
pa
r
ate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Dra
u
g
Bio::Tools:
:
Analysis::Prot
e
in:ELM:
mo
v
e to separ
a
te
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
në Draug
Bio::Too
l
s
:
:Analy
s
is::DNA::ESEfinde
r
:
move
to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë
D
r
a
ug
Bio::DB::RefSeq, B
i
o
:
:DB::EMBL, and subclasses of Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
B
io::Taxonomy:
m
ove dep
r
ec
a
ted namespace to its own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
li
b
/B
i
o
P
erl
.
pm: convert line-ending dos2
u
n
i
x
commit
|
commitdiff
|
tree
2018-09-28
Carn
ë
Draug
doc: update
H
A
CKING instruc
t
i
o
n
s with d
z
il instructions
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
t
/
*: r
e
mo
v
e "u
s
e lib '
.
'" and t/lib/Error
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio::DB::CUTG: move in
t
o
its own di
s
tribution
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
Bio:
:
D
B
::Taxonomy::sqlite:
move i
n
t
o
its own d
i
str
i
b
u
tion
commit
|
commitdiff
|
tree
2018-09-25
Carnë D
r
aug
Bio::DB::GFF move into it
s
own na
m
e
s
pace (e
x
ce
p
t Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carn
ë
Draug
Bio::D
B
::SeqFeature::* m
o
ve
na
m
e
space into its ow
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
C
arnë
D
raug
maint: update chan
g
es from 1f7
b
54a281a
8
commit
|
commitdiff
|
tree
2018-09-25
Carnë
D
raug
B
io::Variation::* mov
e
nam
e
space in
t
o its o
w
n d
i
st
r
ibuti
o
n
.
commit
|
commitdiff
|
tree
2018-09-24
C
a
rnë Draug
Remov
e
Bio::SeqIO s
u
pport fo
r
abi, alf, ctf, exp, pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë Dr
a
ug
Bi
o
::C
l
uster and B
i
o::ClusterIO moved to thei
r
own
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Dra
u
g
B
i
o::Phen
o
type::* move what's left of the namespace
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
maint: remove
n
o longer u
s
e
d
test data files
.
commit
|
commitdiff
|
tree
2018-09-22
Ca
r
në Dr
a
ug
Bio::L
i
veSeq
:
:* move wh
o
le namespace to its
own d
i
stribution
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
maint: update gitignore rules
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
maint: restructu
r
e to use Dist
:
:Zilla
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
t/Al
i
g
nIO/AlignIO
.
t: fix numbe
r
of tes
t
s in plan (fixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
Draug
t/Annotation/Annotation
.
t
: re
m
ove test for Bi
o
::SeqFeatu
r
e
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
Bio/Tools/Run/Phylo
/
PhyloBase
.
p
m: bring base cla
s
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
B
i
o/To
o
ls/Phy
l
o
/
Gu
m
by
.
pm: move to its own
distributi
o
n
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Drau
g
DB/Seq
F
eat
u
re/Store/be
r
keleydb3
.
pm:
f
i
x err
o
rs so it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Adjust tests indirectly making u
s
e
of B
i
o::AlignIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
bp_process_wormbase: move program to new Bio
-
DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
bp_netins
t
al
l
: remo
v
e
out of dat
e
p
r
ogra
m
commit
|
commitdiff
|
tree
2018-09-17
Carnë D
r
a
u
g
M
ove mo
d
ules depe
n
dent on Bio
:
:Ex
t
::
A
l
i
gn into defu
n
c
t
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio
:
:DB::E
x
pression:
m
ove to defun
c
t bioperl-mic
r
oarray
commit
|
commitdiff
|
tree
2018-09-16
Ca
r
në
D
raug
maint: 644 permissi
o
ns f
o
r almost
a
l
l
files
commit
|
commitdiff
|
tree
2018-09-16
Carnë
Draug
maint: set all source code with ut
f
-8 encoding
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
mai
n
t: remove mainta
i
ner out of date f
i
les
commit
|
commitdiff
|
tree
2018-09-16
Carnë D
r
aug
ide: remov
e
module
t
emplates - no
l
onger needed af
t
er
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
C
arnë Dra
u
g
id
e
/bioperl-mode: into its own reposit
o
ry to be dev
e
loped
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë
D
raug
maint: remove biope
r
l-mode release tarballs from
v
er
s
i
on
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
Bi
o
::In
d
ex
:
:A
b
stract-
>
_
t
y
pe_a
n
d_version: che
c
k t
y
pe
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Dra
u
g
t/LocalDB/Index/BlastTable
.
t:
u
se tempdir to avoid
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
t/Loc
a
lDB/Index/Bl
a
st
.
t
:
create test tem
p
f
i
les wi
t
h
i
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carn
ë
D
raug
maint: r
e
move unused test data file
s
commit
|
commitdiff
|
tree
2018-09-14
Carnë
Draug
Remove AlignIO and
Index stockholm
modu
l
es to new
Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
C
a
rnë
Draug
Bio::DB::Universal: move into
it
s
own distribution
commit
|
commitdiff
|
tree
2018-09-14
C
a
rnë Draug
m
a
int: simplify README t
o
c
over simple install instructio
n
s
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë D
r
aug
Bring base cl
a
ss
e
s from BioPe
r
l-run
b
ack to B
i
o
P
erl
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Remove use of Bio::Perl which has
b
een moved
t
o Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
Dra
u
g
Bio::DB
:
:MeSH move
to its own distribution
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dra
u
g
Move HM
M
ER
related modules, tes
t
s, and
programs
t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
B
io::DB::TF
B
S namespace has been moved to its own dist
r
i
b
uti
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Drau
g
Bio::DB::HIV and related modules
and sc
r
ipts
m
oved
.
.
.
commit
|
commitdiff
|
tree
next