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Sync with trunk
2009-01-06
cj
f
ields
S
yn
c
with trunk
commit
|
commitdiff
|
tree
2009-01-05
cjfields
Bum
p
RC to 2; will tag, bag,
a
nd sh
i
p tom
o
r
r
ow after
.
.
.
commit
|
commitdiff
|
tree
2009-01-05
cjfi
e
lds
Sync
with t
r
unk
commit
|
commitdiff
|
tree
2009-01-04
cjfields
sync wit
h
tr
u
nk
commit
|
commitdiff
|
tree
2009-01-02
cjfields
sync from tr
u
nk
commit
|
commitdiff
|
tree
2009-01-02
cjfields
syn
c
last comm
i
t
commit
|
commitdiff
|
tree
2009-01-02
c
j
fiel
d
s
syn
c
with
H
E
AD
commit
|
commitdiff
|
tree
2009-01-02
cjfie
l
ds
R
e
mo
v
e t/G
r
aphi
c
s
commit
|
commitdiff
|
tree
2009-01-02
c
jf
i
elds
R
e
m
ov
e
B
i
o::Gra
p
hi
c
s exa
m
pl
e
s and scripts
commit
|
commitdiff
|
tree
2008-12-26
cj
f
iel
d
s
em
p
t
y
director
y
commit
|
commitdiff
|
tree
2008-12-26
c
j
fields
Em
p
ty directory
commit
|
commitdiff
|
tree
2008-12-26
cjfi
e
lds
empty directory
commit
|
commitdiff
|
tree
2008-12-26
cjfi
e
lds
syn
c
w
i
th trunk
commit
|
commitdiff
|
tree
2008-12-24
cjfields
sm
a
ll clarification
commit
|
commitdiff
|
tree
2008-12-24
c
jfields
Add
list
o
f
bugs slated for
t
h
e
1
.
6
.
x
serie
s
commit
|
commitdiff
|
tree
2008-12-24
c
jfi
e
lds
Updates
for
RC1
commit
|
commitdiff
|
tree
2008-12-24
cjfields
rem
o
ve Microarra
y
d
e
ps
commit
|
commitdiff
|
tree
2008-12-24
cjfields
S
m
all fix for test
s
JIC th
e
re is a network error
commit
|
commitdiff
|
tree
2008-12-24
cjfiel
d
s
S
ync branch
w
i
th
tr
u
nk
commit
|
commitdiff
|
tree
2008-12-24
cjfield
s
Remove Bio::
M
icroarray from branch (st
i
ll in developmen
t
.
.
.
commit
|
commitdiff
|
tree
2008-12-24
cjfiel
d
s
Remove (
m
erge didn't
r
em
o
v
e
thi
s
fo
r
some reason)
commit
|
commitdiff
|
tree
2008-12-24
cjfields
Remo
v
e
(
merge didn'
t
remove this
for some
r
e
a
son)
commit
|
commitdiff
|
tree
2008-12-22
c
j
fields
sync
trunk
with branch
commit
|
commitdiff
|
tree
2008-12-20
cjfiel
d
s
5
.
6
.
1 is min
perl version required for a
l
l
cor
e
modules now
commit
|
commitdiff
|
tree
2008-12-19
cjfi
e
lds
update
N
AMES
commit
|
commitdiff
|
tree
2008-12-19
cjfields
small typo
commit
|
commitdiff
|
tree
2008-12-18
cjfields
t
y
p
o
commit
|
commitdiff
|
tree
2008-12-18
cjf
i
eld
s
[bug 2714]
commit
|
commitdiff
|
tree
2008-12-17
cjfi
e
lds
fix test numb
e
r
commit
|
commitdiff
|
tree
2008-12-17
cj
f
i
elds
up
d
ate
T
est:
:
Warn
(fixes Q
u
al
.
t
t
e
s
t p
r
ob
l
e
m
s with
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cj
f
ields
missed one
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
e
lds
E
U
t
i
lities remote te
s
ts
back online (s
i
mpl
e
test
s
on
l
y)
commit
|
commitdiff
|
tree
2008-12-16
c
jfields
EUtilities rem
o
te
tests back online
(simple
tests only)
commit
|
commitdiff
|
tree
2008-12-16
cjfiel
d
s
Y
ou must actually test dat
a
if y
o
u
want this mo
d
u
le
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjfields
Don'
t
u
s
e print
!
C
h
ang
i
ng to $self-
>
d
ebug or c
o
mmenting o
u
t
commit
|
commitdiff
|
tree
2008-12-16
cjfield
s
Bio::Grap
h
deprecat
e
d i
n
1
.
6
commit
|
commitdiff
|
tree
2008-12-16
cjfields
s
t
i
fl
e
warn
i
ngs when passing string instead of in
t
eger
commit
|
commitdiff
|
tree
2008-12-16
cjfields
hash re
f
, not
a
rr
a
y ref
commit
|
commitdiff
|
tree
2008-12-16
c
j
f
ield
s
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
cjfie
l
ds
[bug
2
6
37]
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
e
lds
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-15
cjf
i
elds
[bu
g
2637
]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
[bug
271
2
]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
scor
e
s
commit
|
commitdiff
|
tree
2008-12-15
cjfields
rem
a
i
n
ing
t
ests
for Bio::Tool
:
:EUtili
t
ies
commit
|
commitdiff
|
tree
2008-12-15
cjfie
l
ds
m
o
re
test
d
ata
commit
|
commitdiff
|
tree
2008-12-15
cjfields
Up
d
ates:
commit
|
commitdiff
|
tree
2008-12-13
c
j
fields
initia
l
bat
c
h of EUtilParameters t
e
sts
commit
|
commitdiff
|
tree
2008-12-13
cjfiel
d
s
einfo tests
commit
|
commitdiff
|
tree
2008-12-12
cjfields
so
m
e EUtil
i
ties tests (
p
arsin
g
from files)
commit
|
commitdiff
|
tree
2008-12-12
cjfields
some test data for
B
i
o::Tool
s
::EUtilities
commit
|
commitdiff
|
tree
2008-12-12
cjfields
upd
a
t
es to
EUtilities (gett
i
ng
rea
d
y fo
r
d
ocs, tests
.
.
.
commit
|
commitdiff
|
tree
2008-12-12
cjfiel
d
s
M
o
ve E
U
tilParame
t
er
s
to Tools (seems
m
ore appropriate)
commit
|
commitdiff
|
tree
2008-12-11
cjfields
f
i
x
for bug when getti
n
g
c
ached
r
es
p
o
n
s
e w
i
th
f
i
lena
m
e
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
small point
e
r
to wik
i
page
(will update along
w
ith
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
sm
a
ll upda
t
e
commit
|
commitdiff
|
tree
2008-12-11
cjfields
u
p
dates
commit
|
commitdiff
|
tree
2008-12-11
cjfields
r
eturn, not
'return undef'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
return, not 'return undef'
commit
|
commitdiff
|
tree
2008-12-11
cjfiel
d
s
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug 2
6
99]
commit
|
commitdiff
|
tree
2008-12-11
cjfi
e
l
d
s
[bug 2707]
commit
|
commitdiff
|
tree
2008-12-10
c
j
f
i
e
ld
s
Removing from HEA
D
(depre
c
a
t
ed
fo
r
1
.
6)
commit
|
commitdiff
|
tree
2008-12-10
cjfield
s
mini
p
o
d fix
commit
|
commitdiff
|
tree
2008-12-10
cj
f
i
e
l
ds
u
p
date deprecation list
commit
|
commitdiff
|
tree
2008-12-10
cjfields
r
emove Bio::Graphics (separate package now)
commit
|
commitdiff
|
tree
2008-12-10
cj
f
ields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cjfield
s
Remo
v
e dependencies for Bio::Gra
p
hic
s
and
d
e
p
recated
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfie
l
ds
Squash warning
commit
|
commitdiff
|
tree
2008-12-09
cjfields
diag() only on verbose
commit
|
commitdiff
|
tree
2008-12-09
c
j
fields
Fix last loop tests,
move some
t
o can_ok
commit
|
commitdiff
|
tree
2008-12-09
cjfields
M
odify to test new temp cla
s
ses an
d
ensure
t
hat ad
d
ed
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
update Mauri
c
io's e
m
ail
commit
|
commitdiff
|
tree
2008-12-08
cj
f
ields
Update Roy's email
commit
|
commitdiff
|
tree
2008-12-08
cjfi
e
lds
Roy's
e
mail (and biop
e
rl
.
o
r
g not bio
p
e
r
l
.
ed
u
)
commit
|
commitdiff
|
tree
2008-12-08
cjf
i
eld
s
U
p
dated
e
m
ails
commit
|
commitdiff
|
tree
2008-12-07
cjfield
s
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-05
cjfie
l
ds
Ne
e
d
to re
t
riev
e
the tr
e
e f
o
r
o
ut
p
ut
commit
|
commitdiff
|
tree
2008-12-05
cjf
i
elds
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-04
cjf
i
elds
Make Tar
g
et a true DBLink
commit
|
commitdiff
|
tree
2008-12-04
cjfield
s
Dire
c
tory
is no longer n
e
eded (Heikki split th
i
s
u
p
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
a
d
d forc
e
_nse tests
commit
|
commitdiff
|
tree
2008-12-03
cjfields
l
eave ID
u
ndefined
i
f it isn't present, bu
t
allow the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove
f
iles accidently adde
d
f
r
om
l
a
s
t c
o
mmit
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Reorganize T
o
ols tes
t
s (nee
d
s some more splitting
)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remov
e
(tests
ar
e
red
u
ndant,
i
n
C
onsed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge tests an
d
re
m
ov
e
r
edundant file
commit
|
commitdiff
|
tree
2008-12-03
c
j
fields
Upd
a
te test count
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge tests
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove redund
a
nt file
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Remove old f
i
les
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
lds
Start To
o
l
s move
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
small upda
t
es
:
commit
|
commitdiff
|
tree
2008-12-03
cjfields
forgot
to i
n
c
r
ement test c
o
unt
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
d
s
Add a couple of tests for seq_id (
s
mall but significant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
c
j
fields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfield
s
[
bug 245
0
]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 24
5
0]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
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