repo.or.cz
/
bioperl-live.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Regexp to match RNA on request only
2012-09-10
F
loren
t
Angly
Regexp
t
o match RNA on request
o
n
l
y
commit
|
commitdiff
|
tree
2012-09-10
F
l
o
rent Ang
l
y
Fi
x
ed indentation
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
R
e
versed probl
e
matic com
m
it 83
3
4d175ff
b
a095a
9
447038d421cac0d
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
Merg
e
branch 'ampl
i
cons'
commit
|
commitdiff
|
tree
2012-09-10
Fl
o
rent Angly
M
e
rge bran
c
h 'mast
e
r' of g
i
thub
.
com:bioper
l
/
b
ioperl
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent
Angly
Removed some comm
e
n
ts
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
C
ompound ID can now includ the strand
commit
|
commitdiff
|
tree
2012-09-10
F
loren
t
Angly
Bio::DB::I
n
dexedBase com
p
l
iance
with Bio::DB
:
SeqI and
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Flore
n
t Angly
Fixed typo
commit
|
commitdiff
|
tree
2012-09-10
Florent A
n
gly
Fixed silly
e
r
ror
commit
|
commitdiff
|
tree
2012-09-10
F
l
o
r
ent Angly
Updated B
i
o::DB::SeqI POD acc
o
rding to info in Bio
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent An
g
ly
Updated Chan
g
es file
commit
|
commitdiff
|
tree
2012-09-10
F
lorent Angly
Explicit
v
a
ria
b
le name i
n
st
e
ad
of Bio/DB/Qual
.
pm
commit
|
commitdiff
|
tree
2012-09-10
Florent Angly
H
a
ndl
e
R
NA and IUPA
C
char
a
cters
in B
i
o::D
B
::Fasta
commit
|
commitdiff
|
tree
2012-09-10
Florent A
n
gl
y
Upd
a
ted Changes file
commit
|
commitdiff
|
tree
2012-09-10
Florent
Angly
Better alph
a
bet detect
i
on method that
honors I
U
PAC
.
.
.
commit
|
commitdiff
|
tree
2012-09-10
Florent
A
ngly
Fasta and Qual o
n
ly
use t
h
e
Inde
x
edBase
b
a
se
commit
|
commitdiff
|
tree
2012-09-10
Florent
A
ng
l
y
POD updat
e
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
POD update
commit
|
commitdiff
|
tree
2012-09-09
Florent A
n
gly
Fixed bug in
t
roduced in r
e
c
e
nt commit
commit
|
commitdiff
|
tree
2012-09-09
F
lorent Angly
m
a
kei
d
l
ogic
i
n Indexe
d
Base
commit
|
commitdiff
|
tree
2012-09-09
Flo
r
e
nt Angly
Added
e
rror
c
h
ecks
o
n Fasta into Qual
commit
|
commitdiff
|
tree
2012-09-09
Florent An
g
ly
Small sim
p
lific
a
tiosn
commit
|
commitdiff
|
tree
2012-09-09
Florent Angl
y
T
es
t
-make
i
d
o
pt
i
on
commit
|
commitdiff
|
tree
2012-09-09
Florent Angl
y
Mo
r
e streamli
n
ing
commit
|
commitdiff
|
tree
2012-09-09
Florent A
n
gly
Suppo
r
t
f
or
s
p
e
cify
i
ng sequence str
a
nd
commit
|
commitdiff
|
tree
2012-09-09
Florent A
n
gly
Usin
g
t
h
e
_
parse
_
co
m
pound
_
id(
)
m
ethod
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Removed a
test be
c
a
u
se method l
e
n
gth()
does not t
a
ke
.
.
.
commit
|
commitdiff
|
tree
2012-09-09
F
l
orent
Angly
S
t
o
ring number of res
i
dues i
n
index file
commit
|
commitdiff
|
tree
2012-09-09
Flor
e
n
t Angly
Fix to avoid a warning
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Variable n
a
me changes
commit
|
commitdiff
|
tree
2012-09-09
Florent Ang
l
y
S
mall
c
hanges
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Renamed
f
unction more appr
o
pri
a
tely
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
More m
e
thods in In
d
exedBase
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Misleading var
i
able name
commit
|
commitdiff
|
tree
2012-09-09
Flo
r
e
n
t Angly
Cos
m
etic ch
a
nges
commit
|
commitdiff
|
tree
2012-09-09
Flo
r
ent Angl
y
S
m
a
l
l changes
commit
|
commitdiff
|
tree
2012-09-09
Flore
n
t A
n
g
l
y
Fixed
a
coup
l
e of typo
s
and worke
d
on consistent i
n
dentaion
commit
|
commitdiff
|
tree
2012-09-09
Florent Angly
Sub to parse compou
n
d
IDs
commit
|
commitdiff
|
tree
2012-09-08
F
l
o
r
ent A
n
gly
Fixed bug affecting B
i
o::DB::S
e
qFeature
commit
|
commitdiff
|
tree
2012-09-08
F
l
or
e
nt
Angly
Fixing
some
f
aili
n
g tests
commit
|
commitdiff
|
tree
2012-09-08
Florent
Angly
Renam
e
d te
s
t
files for consistency
commit
|
commitdiff
|
tree
2012-09-08
Fl
o
r
e
n
t
Angly
P
OD reor
g
anization
commit
|
commitdiff
|
tree
2012-09-08
Florent
Angly
Fixe
d
test
commit
|
commitdiff
|
tree
2012-09-08
Floren
t
A
ngly
POD up
d
a
t
e
commit
|
commitdiff
|
tree
2012-09-08
Fl
o
re
n
t
Angly
Tes
t
h
e
ader()
commit
|
commitdiff
|
tree
2012-09-08
F
l
ore
n
t A
n
g
ly
fh() mo
v
ed to
_fh() in IndexedBa
s
e
commit
|
commitdiff
|
tree
2012-09-08
Florent
An
g
ly
POD update
commit
|
commitdiff
|
tree
2012-09-08
Florent
A
ngly
POD update
commit
|
commitdiff
|
tree
2012-09-08
F
l
o
rent Ang
l
y
PO
D
upda
t
e
commit
|
commitdiff
|
tree
2012-09-08
Florent An
g
ly
Improved tests
commit
|
commitdiff
|
tree
2012-09-07
Florent
A
ngly
POD
update
commit
|
commitdiff
|
tree
2012-09-07
Florent Angly
B
i
g PO
D
update
commit
|
commitdiff
|
tree
2012-09-07
Flo
r
ent Angly
New opt
i
on to rem
o
v
e
index fi
l
e when done
commit
|
commitdiff
|
tree
2012-09-07
F
lorent Angl
y
Mor
e
i
m
provements
commit
|
commitdiff
|
tree
2012-09-07
Florent Angly
Some
more st
r
eaml
i
n
ing
commit
|
commitdiff
|
tree
2012-09-07
Florent
Angl
y
M
o
ved
get_seq_stream to In
d
exedBase
commit
|
commitdiff
|
tree
2012-09-07
F
l
or
e
nt Angly
M
i
gra
t
ing more code to IndexedBase
commit
|
commitdiff
|
tree
2012-09-07
Florent Angly
Code simplificati
o
n
commit
|
commitdiff
|
tree
2012-09-07
Floren
t
A
ngly
Small POD cha
n
ge
commit
|
commitdiff
|
tree
2012-09-07
F
lorent
A
n
gly
M
i
sc change
s
commit
|
commitdiff
|
tree
2012-09-07
Flo
r
e
n
t Angly
User can
s
upply an
arbi
t
rary name f
o
r the inde
x
file
commit
|
commitdiff
|
tree
2012-09-06
Florent
A
ngly
Suppor
t
i
nd
e
xing an arbitrary
set of files
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
Bette
r
error checking
commit
|
commitdiff
|
tree
2012-09-06
Florent
A
ngl
y
Slight cod
e
rearr
a
ngemen
t
commit
|
commitdiff
|
tree
2012-09-06
Florent Angl
y
Support for inde
x
in
g
multiple fil
e
s
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
More modul
a
rit
y
and
code reuse
commit
|
commitdiff
|
tree
2012-09-06
Flor
e
nt
A
ngly
Removed so
m
e t
e
m
porary c
o
de
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
Small
changes
commit
|
commitdiff
|
tree
2012-09-06
F
lorent Angly
Re
m
ove
d
unn
e
eded
p
ragm
a
s
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
Mor
e
Inde
x
e
dBase
wo
r
k
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
Pa
c
k
ing methods insi
d
e IndexedBa
s
e
commit
|
commitdiff
|
tree
2012-09-06
Flo
r
ent Angly
Mo
r
e IndexedBase work
commit
|
commitdiff
|
tree
2012-09-06
Florent Angly
More DB buildin
g
code i
n
IndexedBase
commit
|
commitdiff
|
tree
2012-09-06
Flo
r
ent Angly
Tied hash
interfact
in
I
ndexe
d
B
ase module
commit
|
commitdiff
|
tree
2012-09-05
Fl
o
rent A
n
gl
y
Indexe
d
Base modul
e
commit
|
commitdiff
|
tree
2012-09-05
F
loren
t
Angly
Using Bio
:
:DB
:
:Inde
x
ed::Stream
inst
e
ad of
Bio::DB:
.
.
.
commit
|
commitdiff
|
tree
2012-09-05
F
lo
r
ent Angly
Us
i
ng same
p
acking for Qual as
for Fasta
commit
|
commitdiff
|
tree
2012-09-05
Florent Angly
Handle empty sequences gra
c
efully
commit
|
commitdiff
|
tree
2012-09-05
Florent Angly
Typo f
i
x
commit
|
commitdiff
|
tree
2012-09-05
Flor
e
nt Angly
Bio::DB::Fasta rep
o
r
t
s correct
a
l
p
habet
f
or files with
.
.
.
commit
|
commitdiff
|
tree
2012-09-05
Florent Angly
More error c
h
eckin
g
and
some reorga
n
iza
t
ion
commit
|
commitdiff
|
tree
2012-09-05
F
l
orent Angly
Test updat
e
for Bio::DB::Qual
commit
|
commitdiff
|
tree
2012-09-04
Flo
r
ent Angly
Use
F
ile::Spec for
porta
b
le f
i
le n
a
mes
commit
|
commitdiff
|
tree
2012-09-04
Florent Angly
F
ixed a typo in POD
commit
|
commitdiff
|
tree
2012-08-27
Florent
Angly
Remov
e
d some undef warnings
commit
|
commitdiff
|
tree
2012-08-27
Floren
t
Angly
Remove some temporary code
commit
|
commitdiff
|
tree
2012-08-27
F
l
orent Angly
P
revent warning
'
Su
b
rou
t
i
n
e
path re
d
efine
d
'
commit
|
commitdiff
|
tree
2012-08-27
Flore
n
t
An
g
ly
Us
e
File::Spe
c
::
c
atfi
l
e() for por
t
ab
l
e f
i
lenames
commit
|
commitdiff
|
tree
2012-08-27
Flore
n
t
A
ngly
P
OD update, and retur
n
values f
o
r clarit
y
commit
|
commitdiff
|
tree
2012-08-27
F
lorent An
g
ly
Formatting a
n
d consistent tabulation
commit
|
commitdiff
|
tree
2012-08-25
Florent Angly
Cannot r
e
commend FClone
:
:Fast over
C
lo
n
e because
its
.
.
.
commit
|
commitdiff
|
tree
2012-08-21
Flor
e
nt Angly
Merge branch 'mast
e
r' into am
p
licons
commit
|
commitdiff
|
tree
2012-08-18
Flore
n
t Angly
IUPAC m
a
tches
RNA se
q
uences too
commit
|
commitdiff
|
tree
2012-08-18
Florent Angly
Typo
f
i
xes
commit
|
commitdiff
|
tree
2012-08-08
Florent Angly
C
l
one::F
a
ster as
a faster alte
r
na
t
ive to C
l
o
n
e
.
On
.
.
.
commit
|
commitdiff
|
tree
2012-08-08
Florent Angly
Make Bio::
T
ools::Primer3
use
t
he cl
o
ne() metho
d
from
.
.
.
commit
|
commitdiff
|
tree
2012-08-08
F
l
orent Angly
Documented that Clon
e
and Stora
b
le modu
l
e
s
a
re
used
.
.
.
commit
|
commitdiff
|
tree
2012-08-04
Flore
n
t
A
n
g
ly
Cha
n
ges file update
commit
|
commitdiff
|
tree
2012-08-02
Fl
o
rent Angly
Merge br
a
n
c
h 'master' of
g
ithub
.
com
:
bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
next