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Bio::Seq::SeqWithQuality: remove deprecated class
2019-02-11
C
a
rnë
D
raug
Bio:
:
Se
q
::SeqWithQual
i
ty:
remove dep
r
ecate
d
class
commit
|
commitdiff
|
tree
2019-02-11
Car
n
ë Drau
g
Use
/usr/bin/
p
erl in
s
te
a
d
o
f
e
n
v
eve
n
on examples
commit
|
commitdiff
|
tree
2019-02-11
Carnë Drau
g
doc: fix POD in B
i
o::SeqI
O
::b
s
ml s
o
t
h
at m
a
n can handl
e
i
t
.
commit
|
commitdiff
|
tree
2019-02-11
Carnë Draug
lib/Bi
o
/
T
o
o
ls/Run/R
E
ADME
:
remove file
commit
|
commitdiff
|
tree
2019-02-11
C
a
rnë Dr
a
ug
doc: add NA
M
E section with abstrac
t
to all mo
d
ule
s
POD
commit
|
commitdiff
|
tree
2019-02-08
Carnë Draug
Bio::Sym
b
ol: m
o
v
e
t
o
its own distribution
commit
|
commitdiff
|
tree
2019-02-08
C
a
rnë Draug
doc: fix typ
o
s on do
c
fo
u
nd by Debian
'
s
l
i
ntian
commit
|
commitdiff
|
tree
2019-02-07
C
a
rnë
D
raug
Bio::Root::Roo
t
I
->d
e
precated: fix when no version argument
.
.
.
commit
|
commitdiff
|
tree
2019-02-07
Carnë Draug
Bio::Root::Ro
o
tI:
deprecat
e
depr
e
c
a
ted() method
(i
s
sue
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
C
a
rnë Draug
v1
.
7
.
4
commit
|
commitdiff
|
tree
2019-02-05
Carnë Draug
maint: do n
o
t in
c
lu
d
e tra
v
is configuration on rel
e
a
s
e
commit
|
commitdiff
|
tree
2019-02-05
Carnë Dra
u
g
m
a
in
t
: update Changes
for upcomin
g
release
commit
|
commitdiff
|
tree
2019-02-05
C
a
rn
ë
Drau
g
t/SeqFeature/Gener
i
c
.
t
:
fix typo o
n
requi
r
e
d
module
.
.
.
commit
|
commitdiff
|
tree
2019-02-05
Carnë
Draug
Bi
o
::Root::Test: fix test_network
u
se of Test::Requ
i
resInternet
commit
|
commitdiff
|
tree
2019-02-05
C
a
r
n
ë
Dra
u
g
m
aint
:
fix repository links on met
a
data (i
s
sue #306)
commit
|
commitdiff
|
tree
2019-01-30
Carnë Dr
a
ug
v1
.
7
.
3
commit
|
commitdiff
|
tree
2019-01-29
Carnë Draug
bin
/
bp_genbank2gff3: fix sorting by fe
a
ture type (issue
.
.
.
commit
|
commitdiff
|
tree
2019-01-29
Carnë Draug
Bio::SeqIO::laserge
n
e: move to its o
w
n
d
istribution
commit
|
commitdiff
|
tree
2018-10-03
Carnë
Drau
g
Cha
n
g
es: more details
a
nd philos
o
phy are
on HACKING
.
.
.
commit
|
commitdiff
|
tree
2018-10-03
Carnë Draug
C
hanges: more det
a
ile
d
comple
t
e list of module
s
/dependencies
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë Drau
g
l
ib/BioPerl
.
pm: star
t
conversion
o
f POD
t
o m
a
k
e
use
.
.
.
commit
|
commitdiff
|
tree
2018-10-01
Carnë
D
raug
b
i
n
/bp_biofetch_g
e
nbank_proxy: move to B
i
o-DB-NCBIHel
p
er
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
Bio::
D
B
:
:SwissProt: move
t
o its own distri
b
ution
commit
|
commitdiff
|
tree
2018-10-01
Carnë Draug
Bio::DB::
B
ioFet
c
h: mov
e
to
i
ts own distribution
commit
|
commitdiff
|
tree
2018-09-30
Carnë D
r
a
u
g
A
utomatic
hand
l
ing of VERSION in all modules (is
s
ue
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Car
n
ë Dra
u
g
t/SeqFea
t
ure/Generic
.
t: fix failing
t
est
s
(fixup fd
e
603f22aa)
commit
|
commitdiff
|
tree
2018-09-30
C
a
rnë Draug
bin/bp_fe
t
ch: move r
e
quire of optional modu
l
e
s where
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
C
arnë Draug
Bio::Map::* and Bio::M
a
pIO::*
: move int
o
their ow
n
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
Remove mani
p
ulation
o
f @INC
and use of
lib
-
require
.
.
.
commit
|
commitdiff
|
tree
2018-09-30
Carnë Draug
d
ist
.
i
n
i: make Win32
a
de
p
endency for W
i
n
d
ow
s
only
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Ca
r
në Draug
Bio::SeqIO::agave: move to its own distribution
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
Bio::SeqIO
:
:ch
a
doxm
l
(and fl
y
base_chadoxml): move
t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-29
Carnë Draug
m
a
i
n
t: list Data:
:
Sta
g
:
:
X
M
LWriter as dropped dependency
commit
|
commitdiff
|
tree
2018-09-29
Carnë Dra
u
g
B
io::Seq
I
O::chao
s
xml (and chao
s
): move to their own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
në Dra
u
g
Bio::SeqIO::stride
r
: mo
v
e into its ow
n
distribution
commit
|
commitdiff
|
tree
2018-09-28
C
a
rnë
D
r
a
ug
Bio::T
o
ols
:
:Protparam: move to it
s
own distribut
i
o
n
commit
|
commitdiff
|
tree
2018-09-28
Car
n
ë Draug
maint:
u
pdate and
clean remov
e
d m
o
du
l
es a
n
d de
p
endencie
s
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::DB::SeqVersion: move into it
s
own
distri
b
ution
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio
:
:Too
l
s::SiR
N
A and related m
o
ved to sep
a
rate
d
istributio
n
commit
|
commitdiff
|
tree
2018-09-28
C
a
rnë Draug
Bio
:
:
T
o
ols::Analysis
:
:Pro
t
ein:
m
ove modules into t
h
eir
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Tools::Analysi
s
::Protein::Scansite: mo
v
e to s
e
p
a
rate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio
:
:Tools:
:
A
nal
y
sis::Pro
t
ein:EL
M
: move to separ
a
te
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
C
arnë
D
raug
Bi
o
::Tools::Analysis:
:
DNA:
:
ESEfinder: move
to separate
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
C
a
rnë
Dra
u
g
Bio::DB:
:
RefSeq, Bio::DB::EMBL, and subclasses of Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
Bio::Taxonomy: move deprecated namespace
t
o
i
ts own
.
.
.
commit
|
commitdiff
|
tree
2018-09-28
Ca
r
në Dr
a
ug
lib/Bio
P
e
r
l
.
pm: convert line-ending
dos
2
un
i
x
commit
|
commitdiff
|
tree
2018-09-28
Carnë Draug
doc: upda
t
e
HACKING
instructi
o
ns with dzil
i
nstructions
commit
|
commitdiff
|
tree
2018-09-25
Carnë Dr
a
ug
t/*
:
remove
"
use lib '
.
'" and t/lib/Error
.
pm
commit
|
commitdiff
|
tree
2018-09-25
Carnë
Dra
u
g
B
io::
D
B::CUTG: m
o
ve into
i
ts
o
w
n dist
r
ibution
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
B
io::DB::
T
axonomy:
:
sqlite: move into its own dis
t
ribution
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
B
io::
D
B
:
:GFF move into its own nam
e
s
pace
(except B
i
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Car
n
ë
Dr
a
ug
Bio::DB::SeqFea
t
ure:
:
* move names
p
ace i
n
to its
own
.
.
.
commit
|
commitdiff
|
tree
2018-09-25
Carnë Draug
m
aint
:
update change
s
fr
o
m 1f7b54a281a8
commit
|
commitdiff
|
tree
2018-09-25
Carnë
Draug
Bio::Vari
a
tion::* move n
a
m
e
s
pac
e
into i
t
s
own distr
i
bution
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë Draug
Re
m
ove Bio::SeqIO
s
upport
f
or a
b
i, alf, ctf, exp, pln
.
.
.
commit
|
commitdiff
|
tree
2018-09-24
Carnë
Draug
Bio::
C
l
uster and Bio::Cluster
I
O
m
oved t
o
their
o
wn
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Car
n
ë
Draug
B
i
o
:
:P
h
enotype::
*
move w
h
a
t's left of the namespace
.
.
.
commit
|
commitdiff
|
tree
2018-09-22
Carnë Draug
maint: r
e
m
ov
e
no
long
e
r
u
sed test data
file
s
.
commit
|
commitdiff
|
tree
2018-09-22
Carn
ë
Draug
B
i
o
::LiveSeq::*
m
ove who
l
e na
m
espace to
i
ts ow
n
dist
r
ibuti
o
n
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dra
u
g
m
a
int: u
p
date gitign
o
re
r
u
l
es
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
rau
g
main
t
:
restructure t
o
use Dist::Zilla
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
t/AlignIO/AlignIO
.
t
:
fix n
u
mb
e
r of test
s
in p
l
an
(
f
ixup
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
t/Anno
t
ation/Annotation
.
t: r
e
move test
f
or Bio::SeqFe
a
ture
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bio/Too
l
s/Run/Phylo/PhyloBase
.
p
m
: bring ba
s
e
c
l
ass
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
Bi
o
/Tools/Phy
l
o/G
u
mby
.
p
m: m
o
ve
to its own distribution
commit
|
commitdiff
|
tree
2018-09-17
Carnë Draug
DB/SeqFeature/Store/berkele
y
db3
.
p
m
: fix errors s
o
it
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë Dr
a
ug
A
d
j
u
st tests in
d
irec
t
ly maki
n
g
use of Bio::AlignIO
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
bp_process_wormbase: move program to new
Bio
-
DB-Ace
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Carnë
D
raug
b
p
_
n
et
i
nsta
l
l
: remove out of dat
e
pr
o
gram
commit
|
commitdiff
|
tree
2018-09-17
C
arnë Drau
g
Move modu
l
es dependent on Bio::Ext::
A
lign
i
nto defunct
.
.
.
commit
|
commitdiff
|
tree
2018-09-17
Car
n
ë Draug
B
io::DB::Expression: m
o
v
e to
defunct bio
p
erl-m
i
croarray
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
maint: 644 permissions for
almo
s
t all
fil
e
s
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
mai
n
t: set all
so
u
rce cod
e
w
i
th u
t
f-8 encoding
commit
|
commitdiff
|
tree
2018-09-16
Ca
r
në Draug
maint: remove mai
n
tainer out
of date fi
l
es
commit
|
commitdiff
|
tree
2018-09-16
Carnë Draug
i
d
e
:
remove
m
o
dule templat
e
s - no lo
n
ge
r
needed afte
r
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Dra
u
g
id
e
/bioperl-m
o
de:
i
n
to its own
r
epos
i
to
r
y
to be
de
v
eloped
.
.
.
commit
|
commitdiff
|
tree
2018-09-16
Carnë Dr
a
ug
maint: r
e
move bioperl-mode re
l
e
a
se tarballs f
r
om
v
ersion
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
Bi
o
::Index::Abstrac
t
->_type_and_versi
o
n: c
h
eck type
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Car
n
ë Draug
t/L
o
ca
l
D
B
/Index
/
Bla
s
t
T
able
.
t: use tem
p
dir to avoi
d
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
C
ar
n
ë Dr
a
ug
t/LocalDB/Index/Bla
s
t
.
t: create tes
t
temp
f
iles within
.
.
.
commit
|
commitdiff
|
tree
2018-09-15
Carnë Draug
maint:
r
e
m
ove unused test data files
commit
|
commitdiff
|
tree
2018-09-14
Carnë Drau
g
Remove
AlignIO a
n
d Index
s
tockholm modules to
new Bio
.
.
.
commit
|
commitdiff
|
tree
2018-09-14
Carnë Dr
a
ug
B
io:
:
DB::Universal: move int
o
it
s
own
distributio
n
commit
|
commitdiff
|
tree
2018-09-14
Carnë Draug
maint: simplify README to cover simple i
n
stall instruc
t
ions
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Dra
u
g
Br
i
ng bas
e
clas
s
e
s
from Bi
o
Perl-run back to
BioPerl
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Drau
g
Remove use
o
f Bio::Perl whi
c
h
has
b
een moved to B
i
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë
D
raug
Bio:
:
DB::
M
eSH move to its own dist
r
ibution
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
Move HMME
R
related
modu
l
es, tests
,
and programs
t
o
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë D
r
aug
Bi
o
::DB::TFBS name
s
pace has been moved to i
t
s own distribu
t
i
.
.
.
commit
|
commitdiff
|
tree
2018-09-13
Carnë Draug
B
i
o::DB
:
:HIV and related modul
e
s and scripts m
o
ved
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë Draug
Bi
o
:
:
Al
i
gn:
:
Graphics: move into
i
t
s
o
wn distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë D
r
aug
Bio::Tools::Run::RemoteBlast:
m
ove into a ne
w
distribution
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
Carnë D
r
a
u
g
B
io::Perl: move its own dist
r
ibution nam
e
d
Bio-Procedu
r
al
commit
|
commitdiff
|
tree
2018-09-12
Ca
r
në Draug
Bio::MolEvol::CodonMode
l
:
m
ove
i
nto
i
t separ
a
te repo
.
.
.
commit
|
commitdiff
|
tree
2018-09-12
C
arnë Dr
a
u
g
Bio::SeqIO::entrezgene: m
o
ve to existin
g
Bio-ASN1-entrezgene
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
C
arn
ë
Dr
a
ug
Bio/Re
s
tr
i
ction/*: move to an
o
ther r
e
po with same name
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në Draug
B
i
o
/
T
oo
l
s/Gel
.
pm: move to an
o
ther
r
epo with same name
.
commit
|
commitdiff
|
tree
2018-09-11
Car
n
ë
D
raug
Bio/SeqEvolut
i
o
n/*:
m
ove t
o
anoth
e
r rep
o
w
i
th same
.
.
.
commit
|
commitdiff
|
tree
2018-09-11
Ca
r
në Draug
B
io/
S
tructure/*:
move
t
o another repo with same n
a
me
.
commit
|
commitdiff
|
tree
2018-09-11
Carnë Drau
g
t
/
d
a
t
a
: re
m
ove more test data
files which moved t
o
.
.
.
commit
|
commitdiff
|
tree
next