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[bug 2984] end was calculated based on arbitrary symbols; punt and let LocatableSeq...
2010-07-20
Florent Angly
Bio::
R
oot
:
:I
O
i
n
s
ert() with no
b
ac
k
up file
commit
|
commitdiff
|
tree
2010-07-20
Florent
A
ngly
R
e
mov
e
d wa
r
ni
n
g whe
n
B
io::Assembly::IO::a
c
e parsing
.
.
.
commit
|
commitdiff
|
tree
2010-07-19
Floren
t
Angly
Improve
d
Bio::Asse
m
bly:
:
IO::ace->write_head
e
r
commit
|
commitdiff
|
tree
2010-07-19
F
l
ore
n
t An
g
ly
B
i
o::
R
oot::IO->_
i
n
sert() sp
e
c
i
al
c
ase when inserting
.
.
.
commit
|
commitdiff
|
tree
2010-07-19
F
l
ore
n
t
Angly
New Bi
o
::Root::IO me
t
hod to
i
nsert text a
t
an arbi
t
r
ary
.
.
.
commit
|
commitdiff
|
tree
2010-07-19
Florent
Angly
M
erge branch 'ma
s
ter' of github
.
com:bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-07-09
F
l
o
rent Angly
M
e
rge branch 'ma
s
t
e
r' of g
i
t
h
ub
.
com
:
bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-07-06
Fl
o
r
ent Angly
Merge branch '
m
a
st
e
r' of
github
.
com
:
biope
r
l/b
i
o
p
e
r
l
.
.
.
commit
|
commitdiff
|
tree
2010-06-28
Flor
e
nt Ang
l
y
Merg
e
branch 'master' of githu
b
.
com:bioperl/biop
e
rl
.
.
.
commit
|
commitdiff
|
tree
2010-06-22
Flo
r
e
n
t
An
g
ly
M
o
re robust
creati
o
n
of c
r
os
s
-c
o
n
t
igs
commit
|
commitdiff
|
tree
2010-06-22
Flo
r
ent Angly
R
e
moved te
m
porary debuggin
g
code
commit
|
commitdiff
|
tree
2010-06-22
F
lorent A
n
gly
Fixed typ
o
s in Bio::Assembly::Contig
commit
|
commitdiff
|
tree
2010-06-18
F
l
orent An
g
l
y
Fix fo
r
bug
2
758
commit
|
commitdiff
|
tree
2010-06-18
Florent Angly
Upda
t
ed 'C
h
anges' file
r
egarding as
s
embly imp
r
o
v
ements
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
Florent Angly
More rob
u
st creat
i
on of cross
-
c
ontigs
commit
|
commitdiff
|
tree
2010-06-12
F
lor
e
nt A
n
gly
Merge bran
c
h 'ma
s
t
er'
of github
.
co
m
:bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-06-12
F
l
orent
Angly
Remov
e
d te
m
pora
r
y debugging c
o
de
commit
|
commitdiff
|
tree
2010-06-09
Fl
o
r
e
nt Angly
Fixed
t
ypos in
B
io::Assembly::Co
n
t
i
g
commit
|
commitdiff
|
tree
2010-06-09
Flor
e
nt Angly
Me
r
ge
b
ranc
h
'maste
r
' of git
h
ub
.
c
om:bioperl/bio
p
erl
.
.
.
commit
|
commitdiff
|
tree
2010-06-09
Flor
e
n
t Angly
Bio::Assembly::Tools:
:
ContigSpectrum:
commit
|
commitdiff
|
tree
2010-06-08
Florent Angly
Upda
t
ed
t
est file for phd par
s
e
r
commit
|
commitdiff
|
tree
2010-06-08
Florent Angly
Merg
e
branch 'master' o
f
gith
u
b
.
com:bioperl/b
i
ope
r
l
.
.
.
commit
|
commitdiff
|
tree
2010-06-08
Florent Angly
Reworked B
i
o:
:
SeqIO::
p
hd->next_se
q
s
o
that it is more
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Floren
t
Angly
Merge
branch 'master'
o
f github
.
com:
b
iope
r
l/bi
o
perl
.
.
.
commit
|
commitdiff
|
tree
2010-06-06
F
lore
n
t Angly
ACE writing mo
r
e rob
u
st w
i
t
h
sequences that don't ha
v
e
.
.
.
commit
|
commitdiff
|
tree
2010-06-06
F
l
o
rent Ang
l
y
Mo
r
e robust re
a
ding of co
n
sen
s
u
s
qu
a
liti
e
s in ACE
p
ars
e
r
commit
|
commitdiff
|
tree
2010-06-06
Florent Angly
Fix for the cod
e
t
hat writes
the
consensus qu
a
l
i
t
i
es
.
.
.
commit
|
commitdiff
|
tree
2010-06-06
Florent Angly
Fix in writing ACE contigs: quality array is c
o
pied
.
.
.
commit
|
commitdiff
|
tree
2010-06-06
Flore
n
t
A
n
gly
Merge
b
r
an
c
h 'ma
s
t
er'
of
githu
b
.
com:bioperl/bio
p
erl
.
.
.
commit
|
commitdiff
|
tree
2010-06-06
F
l
or
e
nt
Angly
Fix for consensus
sequence p
a
d
d
i
ng in 454 ACE variant
commit
|
commitdiff
|
tree
2010-06-06
Florent An
g
ly
M
e
rge branch 'master' of github
.
c
o
m
:bioperl
/
bi
o
perl
.
.
.
commit
|
commitdiff
|
tree
2010-06-05
F
l
orent Angly
M
e
rge branch 'master'
of gith
u
b
.
com:
b
ioperl/bio
p
erl
.
.
.
commit
|
commitdiff
|
tree
2010-06-05
Florent Angly
Fix fo
r
the paddin
g
of conse
n
sus sequences for the
.
.
.
commit
|
commitdiff
|
tree
2010-05-30
Florent Angl
y
Padding t
h
e
co
n
sensus sequen
c
e for 454 A
C
E variant
commit
|
commitdiff
|
tree
2010-05-20
Florent
A
n
g
ly
Writin
g
assembly files (ace, tigr) at once
or
a contig
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
Florent
A
n
gly
Mer
g
e bran
c
h '
m
ast
e
r' of gi
t
@github
.
com:biope
r
l/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-19
Florent An
g
ly
C
h
an
g
e
i
n Bi
o
:
:
Assembly:
:
IO::ace logic
to rem
o
ve
w
arnings
.
.
.
commit
|
commitdiff
|
tree
2010-05-18
F
l
orent Angly
Upda
t
e
d
.
/
C
hanges regard
i
ng t
h
e 454 Newbler ACE variant
commit
|
commitdiff
|
tree
2010-05-18
Flo
r
ent A
n
g
l
y
Implement
e
d th
e
454 Ne
w
bler ACE assembly variant
commit
|
commitdiff
|
tree