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remove multi-declaration warning
2013-09-02
Florent Ang
l
y
Use 'exists', not 'defined', to chec
k
fo
r
existence
.
.
.
commit
|
commitdiff
|
tree
2013-09-02
Florent Angly
Test fixes f
o
r Bio:
:
Assem
b
ly::Tools::ContigSp
e
ctrum
commit
|
commitdiff
|
tree
2013-09-02
Florent Angly
Fixed som
e
"undefined
value" warnings when taxonomy
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Flor
e
n
t Angly
Fixed bug w
h
e
re not
a
ll nodes in lineage
were merged
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Fl
o
re
n
t Angly
More tests
commit
|
commitdiff
|
tree
2013-07-12
Flor
e
nt Angly
Bette
r
disti
n
guish ambiguous t
a
x
o
n names
commit
|
commitdiff
|
tree
2013-07-12
F
l
o
r
ent Angly
Fixed
issue wher
e
am
b
iguous taxa nam
e
s got t
h
e same
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
Fixed bug where
taxon rank w
a
s mis
s
ing
commit
|
commitdiff
|
tree
2013-07-12
Flore
n
t Angly
Mo
r
e Bio::DB::Taxon
o
m
y
::list te
s
ts
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
B
o
o
l
e
an
r
e
turn
s
tatu
s
for merg
e
_lineage
(
)
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
Fixed number of
t
est
s
in
t
/C
l
u
s
te
r
IO/S
e
q
uenceFamily
.
t
commit
|
commitdiff
|
tree
2013-07-12
Florent A
n
gly
Fixed use of uninitial
i
zed v
a
lue
$reporttype
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
Fixe
d
redefined v
a
riab
l
e
commit
|
commitdiff
|
tree
2013-07-12
Florent
Angly
Small
POD
a
nd and error m
e
ss
a
ge cha
n
ge
commit
|
commitdiff
|
tree
2013-07-12
Florent
A
ngly
A
d
ding arbitrary
branch length in B
i
o::D
B
::Taxonomy
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Florent
Angly
Use
a
default format for as_s
t
r
i
ng
commit
|
commitdiff
|
tree
2013-07-12
Fl
o
re
n
t
An
g
l
y
Test
uses spe
c
ies,
n
ot intermedi
a
ry node
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
A
void use of a
n
unde
f
ined va
l
ue as
an ARRAY r
e
fer
e
nce
commit
|
commitdiff
|
tree
2013-07-12
Florent Angly
Use list context instead
of
s
ca
l
ar con
t
ext to include
.
.
.
commit
|
commitdiff
|
tree
2013-07-12
Flor
e
n
t
A
n
gly
Fixed
P
OD i
n
dentation
commit
|
commitdiff
|
tree
2013-07-12
F
l
orent Ang
l
y
Tes
t
s
f
or
B
io::Taxonomy::get
_
tree
commit
|
commitdiff
|
tree
2013-07-11
Florent Angly
More thoroughly documen
t
e
d options
a
nd defaults
commit
|
commitdiff
|
tree
2013-07-11
Flore
n
t Angly
Restoring intende
d
behaviour
.
.
.
I
t
hink
commit
|
commitdiff
|
tree
2013-07-11
Florent
A
ngly
Fixed failing DBD test
commit
|
commitdiff
|
tree
2013-02-03
Florent A
n
gly
F
i
x
e
d
POD enco
d
ing
issue
commit
|
commitdiff
|
tree
2012-11-18
F
l
ore
n
t Angly
M
e
rge branch 'maste
r
' of github
.
com:b
i
op
e
r
l/
b
ioperl
.
.
.
commit
|
commitdiff
|
tree
2012-11-17
Fl
o
rent Angly
Merge branc
h
'm
a
s
ter' in
t
o bug
_
33
9
0
commit
|
commitdiff
|
tree
2012-11-17
Florent Angly
Tightened and optimized qua
l
ity str
i
ng valid
a
tion
commit
|
commitdiff
|
tree
2012-11-17
Florent A
n
gly
U
p
d
a
ted planned
n
u
m
ber of t
e
sts
commit
|
commitdiff
|
tree
2012-11-17
Florent An
g
l
y
'
our' is
p
referre
d
over '
u
se va
r
s'
commit
|
commitdiff
|
tree
2012-11-17
Flor
e
nt Angly
Test up
d
ates (Pri
m
aryQual
m
os
t
ly
)
commit
|
commitdiff
|
tree
2012-11-17
Flor
e
nt Angl
y
Pr
i
marySeq validation speedup
commit
|
commitdiff
|
tree
2012-11-16
Flore
n
t A
n
gly
I
n
stead of closures, simply s
t
or
e
at
t
ributes in $se
l
ft
commit
|
commitdiff
|
tree
2012-11-15
Flore
n
t
A
ngl
y
Merge branch 's
e
q
l
en
g
th'
commit
|
commitdiff
|
tree
2012-11-09
F
l
o
r
en
t
Angly
Updated num
b
er
o
f
t
e
s
ts
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
Primar
y
Qual validation sy
n
chronized with that of P
r
ima
r
ySe
q
commit
|
commitdiff
|
tree
2012-11-06
F
l
orent Ang
l
y
S
ame
revcom() and length()
a
pproac
h
in B
i
o::D
B
::Qu
a
l
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Flor
e
nt
A
n
gl
y
New l
e
n
g
th() method neeed to co
n
sider strandedness
commit
|
commitdiff
|
tree
2012-11-06
Flore
n
t
Angly
Also r
e
v
ert to ol
d
revcom() +
test +
do
c
commit
|
commitdiff
|
tree
2012-11-06
F
l
orent
Angly
R
everted to previous
b
ehavi
o
ur, i
.
e
.
o
v
e
r
r
i
de Pri
m
aryS
e
qI
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Flore
n
t
Ang
l
y
Mer
g
e bra
n
c
h
'm
a
ster' of githu
b
.
com:bioper
l
/bioperl
.
.
.
commit
|
commitdiff
|
tree
2012-11-06
Flor
e
n
t Angly
B
i
o::DB::length
i
mproveme
n
t
commit
|
commitdiff
|
tree
2012-11-06
Flore
n
t Angly
Bio::PrimaryQual PO
D
update
commit
|
commitdiff
|
tree
2012-11-06
F
l
orent A
n
gly
More Bio::DB::Qual
t
ests
commit
|
commitdiff
|
tree
2012-11-06
F
l
orent Angly
Le
t
PrimarySeqI han
d
le revcom() and trunc()
commit
|
commitdiff
|
tree
2012-11-06
Florent Angly
Te
s
t Bio::Pr
i
m
a
ry
S
e
q
::Fasta
complian
c
e wit
h
B
i
o
:
:Prima
r
ySeqI
commit
|
commitdiff
|
tree
2012-11-05
Fl
o
r
ent Angly
Mor
e
tests
commit
|
commitdiff
|
tree
2012-11-05
Flor
e
nt Angl
y
A
dded a te
s
t
commit
|
commitdiff
|
tree
2012-11-05
Florent An
g
ly
C
osmetic chang
e
S
commit
|
commitdiff
|
tree
2012-11-05
Florent An
g
l
y
Redund
a
n
t
messages
commit
|
commitdiff
|
tree
2012-11-05
Fl
o
rent
A
ngly
v
alidate_seq() takes
a
s
t
ring as
a
rgument
commit
|
commitdiff
|
tree
2012-11-05
Flo
r
ent
A
ngly
undef sequen
c
e strings
are valid sequences
commit
|
commitdiff
|
tree
2012-11-05
F
lorent Angly
Small fix
commit
|
commitdiff
|
tree
2012-11-05
F
lore
n
t
A
n
gly
Redundant seq
u
ence val
i
dation
commit
|
commitdiff
|
tree
2012-11-05
Florent Angl
y
Co
s
metic
changes, ind
e
n
t
a
t
ion, e
t
c
commit
|
commitdiff
|
tree
2012-11-05
Flore
n
t
Angly
Avoid
w
a
r
ning me
s
sage durin
g
testing
commit
|
commitdiff
|
tree
2012-11-01
Florent Angly
Har
d
ening test
commit
|
commitdiff
|
tree
2012-11-01
Florent Angly
F
i
x f
o
r
r
egression bu
g
#3
3
90
commit
|
commitdiff
|
tree
2012-11-01
Flor
e
nt Angly
Update
d
t
ests for Bio
:
:DB::Fasta
commit
|
commitdiff
|
tree
2012-10-31
Florent
A
n
g
ly
Added test
f
or
b
u
g 339
0
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Add
e
d
tests that u
s
e the fil
e
(
) metho
d
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
e
nt
Angly
Changes
f
i
le update
commit
|
commitdiff
|
tree
2012-10-31
Florent
Angly
Ch
a
nge
s
update
commit
|
commitdiff
|
tree
2012-10-31
Florent
An
g
ly
-direct
v
alid
o
nly once
commit
|
commitdiff
|
tree
2012-10-31
Florent
A
ngly
s
u
bs
e
q() speedup
commit
|
commitdiff
|
tree
2012-10-31
F
l
orent Angly
More length() tes
t
s
and some POD up
d
at
e
commit
|
commitdiff
|
tree
2012-10-31
Flo
r
e
nt Angly
Removed som
e
co
d
e redundancy
commit
|
commitdiff
|
tree
2012-10-31
Florent A
n
gly
Bio::Primar
y
SeqI speedu
p
commit
|
commitdiff
|
tree
2012-10-31
Flore
n
t
Angly
Cosmet
i
c
changeS
commit
|
commitdiff
|
tree
2012-10-31
Flor
e
nt Angly
Cosmeti
c
change
s
commit
|
commitdiff
|
tree
2012-10-31
Florent
A
n
gly
Avoid new() ju
s
t
to revcom() a sequence
commit
|
commitdiff
|
tree
2012-10-31
Flor
e
nt An
g
ly
Subseq() optimisati
o
n
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
Angly
Tes
t
ing subs
e
q()
more thoroughly
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
More te
s
ts for
val
i
d
ate_se
q
()
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Testing vali
d
at
e
_seq() an
d
-ref
_
to_seq
commit
|
commitdiff
|
tree
2012-10-31
Florent Angly
Cons
t
ruct
o
r
-re
f
_t
o
_
s
e
q
f
i
x
commit
|
commitdiff
|
tree
2012-10-31
F
lorent Angly
Small changes
i
n seq()
for clari
t
y
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
Angly
Small fix in validat
i
on er
r
or m
e
ssa
g
e
commit
|
commitdiff
|
tree
2012-10-31
Fl
o
rent Angly
Prim
a
rySeq::seq() modularization
commit
|
commitdiff
|
tree
2012-10-31
Flore
n
t
A
ngly
Removed
unne
e
de
d
method
commit
|
commitdiff
|
tree
2012-10-31
Floren
t
Angly
POD update and more consi
t
ent
varia
b
le names
commit
|
commitdiff
|
tree
2012-10-30
Florent Ang
l
y
PrimarySeq
d
irect mode
fix/improvement
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Small
P
OD and tes
t
s u
p
dates
commit
|
commitdiff
|
tree
2012-10-30
Florent A
n
gly
D
o
c
fixe
s
commit
|
commitdiff
|
tree
2012-10-30
Florent Ang
l
y
More
t
ests for PrimarySeq
commit
|
commitdiff
|
tree
2012-10-30
Florent
A
n
g
ly
Fix
e
s issue
in Enc
o
d
edSeq
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
C
osmetic changes
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Consistent inde
n
t
a
tion
commit
|
commitdiff
|
tree
2012-10-30
Flore
n
t
A
n
g
ly
SeqF
a
staSpeedFa
c
tory fix
commit
|
commitdiff
|
tree
2012-10-30
Florent Angly
Consistent indentation
commit
|
commitdiff
|
tree
2012-10-30
Flor
e
nt
A
ngly
Bio::PrimarySeq::leng
t
h() opti
m
iza
t
ion
s
commit
|
commitdiff
|
tree
2012-10-30
F
l
orent
A
ngly
More
test
s
for Bio::PrimarySeq::length()
commit
|
commitdiff
|
tree
2012-10-30
Florent A
n
gl
y
PO
D
updated and
beautification
commit
|
commitdiff
|
tree
2012-10-30
Florent
A
ngly
Mor
e
tests fo
r
B
io::P
r
imarySeq::length()
commit
|
commitdiff
|
tree
2012-10-30
Florent Ang
l
y
A
d
de
d
te
s
ts for Bio::PrimaryS
e
q::
l
engt
h
()
commit
|
commitdiff
|
tree
2012-10-29
Fl
o
rent Angly
Fix for bug #3389
commit
|
commitdiff
|
tree
2012-10-29
Florent Ang
l
y
P
rimarySeq::l
e
ngth() speedu
p
commit
|
commitdiff
|
tree
2012-10-10
Florent Ang
l
y
Better
0-
l
e
n
gth
seque
n
ce suppor
t
for
B
io::D
B
::Qual
.
.
.
commit
|
commitdiff
|
tree
2012-10-10
Florent Angly
B
e
t
t
er support for
0
-length se
q
uences
commit
|
commitdiff
|
tree
2012-09-24
Florent Angly
Merge branch '
m
aster' of github
.
com:bioperl/bio
p
erl
.
.
.
commit
|
commitdiff
|
tree
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