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hmmer3.pm: Fixed a bug where an homology line ending in CS or RF
2013-12-15
Fra
n
cis
c
o J
.
Oss
a
n
d
on
LocalDB/Fas
t
a
.
t: Removing le
f
tover temporal files
.
commit
|
commitdiff
|
tree
2013-12-15
Fran
c
isco J
.
O
s
sandon
B
ioDBGFF
.
t: Most of the t
e
sts
can
b
e handled fin
e
by
.
.
.
commit
|
commitdiff
|
tree
2013-12-15
F
r
ancisco J
.
Ossandon
LoadHelpe
r
.
pm: Some temporal fi
l
es are not delet
e
d
.
.
.
commit
|
commitdiff
|
tree
2013-12-11
Francisco
J
.
Oss
a
ndon
Bio/SearchIO/SearchRe
s
ult
E
v
e
ntBuilder
.
pm: A
v
oid adding
.
.
.
commit
|
commitdiff
|
tree
2013-12-10
Franc
i
s
co J
.
Ossandon
Bio/Inde
x
/
Fasta
.
pm:
R
em
o
ved a
fi
x
ed offset adj
u
stmen
t
.
.
.
commit
|
commitdiff
|
tree
2013-12-10
Francisco J
.
O
s
san
d
on
Bio/DB/Flat/BD
B
.
pm: Wi
n
dows
o
ffset adjustment
c
ode
.
.
.
commit
|
commitdiff
|
tree
2013-12-06
Francisco J
.
Ossando
n
Bio::SeqIO:
:
fasta
.
pm: Replace chom
p
for s/
/
/
since
.
.
.
commit
|
commitdiff
|
tree
2013-12-04
Francisco J
.
Ossan
d
on
Bi
o
/SearchIO/Bla
s
t
.
pm: Removed
tabs
commit
|
commitdiff
|
tree
2013-12-04
F
ran
c
i
sco
J
.
Ossandon
Bio/SearchIO
/
blast
.
pm: Fixed bug #2978
.
Added
a c
o
d
e
.
.
.
commit
|
commitdiff
|
tree
2013-11-25
F
r
ancisco J
.
Os
s
and
o
n
Bio/SeqIO/inter
p
ro
.
pm: Recognition of '<pro
t
e
in>
'
is
.
.
.
commit
|
commitdiff
|
tree
2013-11-23
Franc
i
sco J
.
Ossandon
R
emoved tabs fr
o
m
p
revious commit
commit
|
commitdiff
|
tree
2013-11-23
F
r
anci
s
c
o
J
.
Ossandon
Bio/SimpleAli
g
n
.
pm: Fixed a TODO, all
o
w
ed th
e
u
s
e of
.
.
.
commit
|
commitdiff
|
tree
2013-11-22
Francisco
J
.
Ossandon
Untabified 't
/
Local
D
B
/
I
n
dex/Index
.
t' an
d
del
e
ted som
e
.
.
.
commit
|
commitdiff
|
tree
2013-11-22
Franc
i
sco J
.
Ossandon
Big Windows compatibi
l
ity f
i
xes
.
Now all tes
t
s pas
s
.
.
.
commit
|
commitdiff
|
tree
2013-11-21
F
r
ancisco J
.
Ossandon
B
i
o/Index/Blast
:
Fixed _index_file to adj
u
st fileha
n
dle
.
.
.
commit
|
commitdiff
|
tree
2013-11-21
Francisco J
.
O
ssandon
Bio/SearchIO/
b
lasttable: Recover
c
onserv
e
d value from
.
.
.
commit
|
commitdiff
|
tree
2013-11-21
Francis
c
o J
.
Ossan
d
on
Bio/As
s
embly/S
i
ng
l
et: Get End fr
o
m
p
a
r
e
nt
seq
u
ence
.
.
.
commit
|
commitdiff
|
tree
2013-11-21
Fr
a
ncisco J
.
Ossandon
B
io
/
I
n
d
ex/Abstract
:
Fix
e
d uninitial
i
zed
w
ar
n
ing f
r
om
.
.
.
commit
|
commitdiff
|
tree
2013-11-20
Francisco J
.
Ossandon
Merge pull request #54
f
rom fjossa
n
don/m
a
ster
commit
|
commitdiff
|
tree
2013-11-11
Fr
a
ncisco J
.
Os
s
ando
n
Bio/SeqFeat
u
r
e/Generic
.
pm: Fixed uninitialize
d
warnings
commit
|
commitdiff
|
tree
2013-11-11
Francisco
J
.
O
s
sandon
t/Seq
F
e
a
ture
/
Generic
.
t
: Fixed a t
e
st
o
f ci
r
cular sequences
.
.
.
commit
|
commitdiff
|
tree
2013-11-11
Fra
n
cisco
J
.
Ossandon
Bi
o
/SeqFeature/Generic
.
pm: U
p
dated Start, End and
Length
.
.
.
commit
|
commitdiff
|
tree
2013-11-08
Fran
c
isco J
.
Ossandon
Bio/DB/Fasta
.
pm: Sma
l
l
Windows compatibility fi
x
in
.
.
.
commit
|
commitdiff
|
tree
2013-11-08
Franci
s
co J
.
Ossan
d
on
Bio/S
e
q
FeatureI
.
pm
:
Changes
t
o spl
i
c
ed_seq sequen
c
e
.
.
.
commit
|
commitdiff
|
tree
2013-11-08
Francisco J
.
Oss
a
ndon
B
i
o
/
Factory/FTLocati
o
nFactor
y
.
pm: Refined
l
o
g
ic for
.
.
.
commit
|
commitdiff
|
tree
2013-11-08
Fr
a
ncisco J
.
Ossandon
M
e
r
ge
remote branch
'upstream/master' into test
commit
|
commitdiff
|
tree
2013-09-22
Francisco J
.
O
s
sa
n
don
Bio/Primary
S
eq
.
pm: Fixed some 'uni
n
itialized
value
.
.
.
commit
|
commitdiff
|
tree
2013-09-22
Francisc
o
J
.
Os
s
ando
n
Merge remot
e
b
ranch
'
upst
r
e
a
m/ma
s
ter' in
t
o t
e
st
commit
|
commitdiff
|
tree
2013-09-22
Fra
n
cisco J
.
Ossandon
Bio/SeqUtils: trun
c
_with_features() an
d
revcom_with
_
f
eatures()
commit
|
commitdiff
|
tree
2013-09-22
Francisc
o
J
.
Ossandon
Fi
x
typing
e
rrors
commit
|
commitdiff
|
tree
2013-09-18
F
rancisco
J
.
Ossand
o
n
FTL
o
cationFactory
.
pm: Fix in f
r
om_string() for some
.
.
.
commit
|
commitdiff
|
tree
2013-09-17
Francisc
o
J
.
O
s
sandon
P
rimaryS
e
qI
.
pm: Avoid using
Bi
o
::Root::clone when objec
t
commit
|
commitdiff
|
tree
2013-09-17
Francisc
o
J
.
Ossan
d
on
M
e
r
g
e remote
b
ranch 'up
s
tr
e
am/maste
r
' into test
commit
|
commitdiff
|
tree
2013-04-18
Francisco J
.
O
s
s
andon
Pr
i
m
a
r
ySeq
.
t: TODO te
s
t
s
are no
w
fixed
.
All the other
.
.
.
commit
|
commitdiff
|
tree
2013-04-18
Francisco
J
.
Ossandon
P
r
imarySeqI
.
pm: use Bi
o
::Root::clone to
make sure th
a
t
.
.
.
commit
|
commitdiff
|
tree
2013-04-18
Franc
i
sco J
.
Os
s
a
ndon
PrimarySe
q
.
pm/new: Cha
n
g
e
d $is_c
i
rcular test to use
.
.
.
commit
|
commitdiff
|
tree
2013-04-18
Fra
n
c
isco J
.
Ossandon
Merge remo
t
e branch '
u
pstream/master
'
commit
|
commitdiff
|
tree
2013-04-15
Francisco
J
.
Ossandon
Me
r
ge remote branch 'upstr
e
a
m/master'
commit
|
commitdiff
|
tree
2013-04-15
Francisco J
.
Ossandon
E
x
p
a
nded
s
ome comments
commit
|
commitdiff
|
tree
2013-04-15
Francis
c
o J
.
O
ssando
n
Added extens
i
ve
t
est
i
ng for
t
he
introduced changes
.
.
.
commit
|
commitdiff
|
tree
2013-04-15
Fran
c
isco J
.
Ossandon
PrimaryS
e
q/s
u
bseq now
uses "guide_strand" for S
p
lit
.
.
.
commit
|
commitdiff
|
tree
2013-04-15
F
rancisco J
.
Oss
a
ndon
Split/to_FTstring don't nee
d
to reverse sublocations
.
.
.
commit
|
commitdiff
|
tree
2013-04-15
Francisco J
.
Ossandon
Spli
t
/guide_s
t
rand now ma
k
es
a
consistency check
o
f
.
.
.
commit
|
commitdiff
|
tree
2013-04-15
Francisco J
.
Ossandon
Split/flip_stra
n
d now makes
a
str
a
nd con
s
iste
n
cy check
.
.
.
commit
|
commitdiff
|
tree
2013-04-15
Fr
a
n
c
isco
J
.
Ossan
d
on
Initiali
z
e the Strand value if mi
s
s
ing before performin
g
.
.
.
commit
|
commitdiff
|
tree
2013-03-15
Francis
c
o
J
.
O
ssandon
Fix for Bug #
2
9
36,
n
o
w
S
p
lit
.
pm
/
f
lip_strand
sets guide
_
stran
.
.
.
commit
|
commitdiff
|
tree
2013-03-07
F
r
ancisco J
.
Ossand
o
n
Fix for Bug #3251, plus
f
ixed a coupl
e
of
r
egu
l
a
r
expression
.
.
.
commit
|
commitdiff
|
tree
2013-03-07
F
ran
c
isco J
.
Ossandon
Revert
"Fixed
n
o-hit blast bug and
f
aulty regexs,
added
.
.
.
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