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sync with trunk
2009-09-30
cjfields
syn
c
wi
t
h
t
runk
commit
|
commitdiff
|
tree
2009-09-29
cjf
i
el
d
s
sync with
main trunk
commit
|
commitdiff
|
tree
2009-02-25
cj
f
ields
m
erge la
s
t commi
t
t
o
b
ranch
commit
|
commitdiff
|
tree
2009-02-24
cjfiel
d
s
b
ump version
commit
|
commitdiff
|
tree
2009-02-24
c
j
fields
s
y
nc
wit
h
trunk
commit
|
commitdiff
|
tree
2009-02-11
c
j
fie
l
ds
s
ync with trunk
commit
|
commitdiff
|
tree
2009-02-01
cjfiel
d
s
b
r
anch-sp
e
c
i
fic versioning
commit
|
commitdiff
|
tree
2009-02-01
cjfi
e
lds
syc w
i
th trunk
commit
|
commitdiff
|
tree
2009-01-28
c
jfields
forgo
t
to change v
e
rsioning
,
will retag
commit
|
commitdiff
|
tree
2009-01-28
cjfields
sync with run trunk
commit
|
commitdiff
|
tree
2009-01-13
cjfields
*
small u
p
dat
e
s
commit
|
commitdiff
|
tree
2009-01-13
cjf
i
eld
s
Re
m
ove Pise-
r
elated st
u
ff
,
u
pd
a
t
e with o
t
h
er dependencies
commit
|
commitdiff
|
tree
2009-01-13
cjfie
l
d
s
Add
D
EPENDENCIES file
.
commit
|
commitdiff
|
tree
2009-01-13
cjfields
R
e
move
P
ise-related ex
a
mple
s
(moved into bioperl-
p
ise)
commit
|
commitdiff
|
tree
2009-01-13
cjfie
l
ds
R
em
o
ve Pise-rela
t
ed m
o
dule (moved
i
nto bioperl-pise)
commit
|
commitdiff
|
tree
2009-01-13
cj
f
ields
Remove
P
ise modules
a
n
d tests (moved into
b
ioperl-pise)
commit
|
commitdiff
|
tree
2009-01-13
cjf
i
el
d
s
Remove Pise modu
l
es and tests (moved into bioperl-pise)
commit
|
commitdiff
|
tree
2009-01-10
cj
f
ields
Don't TODO
the test, a
c
tual
l
y
attemp
t
to
run it and
.
.
.
commit
|
commitdiff
|
tree
2009-01-10
cjfields
Actual
l
y
make t
e
sts
c
o
m
plete (not skipped if there
.
.
.
commit
|
commitdiff
|
tree
2009-01-10
cjfie
l
d
s
TO
D
O failing test (problem w
i
th SOA
P
protocol
)
commit
|
commitdiff
|
tree
2009-01-10
c
j
fie
l
d
s
* finish
u
p bioperl-
r
un
c
on
v
ers
i
on
commit
|
commitdiff
|
tree
2009-01-08
cjfields
requi
r
es
not required
commit
|
commitdiff
|
tree
2009-01-08
cjf
i
elds
* conve
r
t
o
ver to
B
i
o::Root::Test
and update some t
o
.
.
.
commit
|
commitdiff
|
tree
2009-01-08
cjfields
* convert to Bio:
:
Root
:
:Test
commit
|
commitdiff
|
tree
2009-01-08
cjfi
e
ld
s
* conver
t
t
o
Bio::Roo
t
:
:Test
commit
|
commitdiff
|
tree
2009-01-07
cjfields
Ge
t
t
ing a fail
e
d test using lat
e
st EnsEMBL p
e
rl AP
I
.
.
.
commit
|
commitdiff
|
tree
2009-01-07
cjfields
Catch ve
r
sion
,
skip tests if
v
ersion isn'
t
supported
.
.
.
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[bug
2
644]
commit
|
commitdiff
|
tree
2008-08-22
cjfields
* add_sequences op
t
ion (adds sequences
t
o
a
n al
i
gnment
.
.
.
commit
|
commitdiff
|
tree
2008-07-30
cjfi
e
lds
patching the cor
r
e
ct Primer3
.
pm (not Bio::Tools::Pr
i
mer3
.
pm)
commit
|
commitdiff
|
tree
2008-06-19
cjfields
bug 2523
commit
|
commitdiff
|
tree
2008-04-15
cjfields
Upd
a
t
e t
o
0
.
81 params
.
Need to set up test
s
for this
.
.
.
commit
|
commitdiff
|
tree
2008-02-27
cjfiel
d
s
bug 2460
commit
|
commitdiff
|
tree
2008-01-15
cjfie
l
ds
te
s
t
commit
|
commitdiff
|
tree
2007-07-16
cjfields
bug 2202
commit
|
commitdiff
|
tree
2007-07-16
cjfields
bug 2299
commit
|
commitdiff
|
tree
2007-07-01
cjf
i
elds
bug 2299
commit
|
commitdiff
|
tree
2007-04-02
cjfields
w
r
a
pper for
tRNAscanSE
commit
|
commitdiff
|
tree
2007-03-30
cjfields
small f
i
x: RNAMo
t
if can
have
empty
f
i
l
es (will add
.
.
.
commit
|
commitdiff
|
tree
2007-03-29
c
jfiel
d
s
f
i
x some
f
unkiness w
i
th
p
ipes; may
s
witch to IPC::Run
.
.
.
commit
|
commitdiff
|
tree
2007-03-20
c
j
f
i
elds
All inferna
l
p
ro
g
rams now wor
k
; nee
d
s some
m
ore fine
.
.
.
commit
|
commitdiff
|
tree
2007-03-19
cjfields
bug
2241
commit
|
commitdiff
|
tree
2007-03-14
cjfie
l
ds
small
fixes
commit
|
commitdiff
|
tree
2007-03-13
cj
f
ields
IP
C
::Run (
r
equired for Glimmer, Genemark wrappers)
commit
|
commitdiff
|
tree
2007-03-13
cjfield
s
G
en
e
Ma
r
k, Gl
i
mmer wrapper modules, tests, and t
e
st
.
.
.
commit
|
commitdiff
|
tree
2007-02-17
cjfields
cmsearch nows
w
orks;
rest
hopefu
l
l
y
by
M
on
.
commit
|
commitdiff
|
tree
2007-02-16
cjfi
e
l
ds
In
f
ernal wrapper (not fun
c
tio
n
al yet)
commit
|
commitdiff
|
tree
2007-02-07
cjfields
u
p
dates and small tweaks
commit
|
commitdiff
|
tree
2007-02-07
cjfields
erpin wra
p
per
(nee
d
s more wo
r
k
.
.
.
)
commit
|
commitdiff
|
tree
2007-02-05
cjfield
s
Allow outfil
e
or te
m
pfile (for downstre
a
m
work)
commit
|
commitdiff
|
tree
2007-02-04
cjfield
s
o
bscure origin
s
a bit mor
e
(he
h
ehe
commit
|
commitdiff
|
tree
2007-02-04
cjfields
RNAMotif tools wrapper
commit
|
commitdiff
|
tree
2006-10-26
cj
f
ields
Change to
Test:
:
More
commit
|
commitdiff
|
tree
2006-10-26
cjfields
Add Test
:
:More
(appa
r
ently
w
asn't added)
commit
|
commitdiff
|
tree
2006-10-26
cjf
i
el
d
s
Add some POD for CLOSE()
commit
|
commitdiff
|
tree
2006-10-26
cjfields
Add
e
d CLOSE()
t
i
e
d fi
l
ehandle method
(
bu
g
212
6
)
commit
|
commitdiff
|
tree
2006-10-13
cjfields
Revert tests; repeated ca
l
ls now work (ex
p
ected behavior)
commit
|
commitdiff
|
tree
2006-10-10
c
j
fields
Fix te
s
ts; need to look at Analysis::soap:
:
re
s
ults()
commit
|
commitdiff
|
tree
2006-07-11
cjfiel
d
s
Bug 2040
commit
|
commitdiff
|
tree