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Remove (merge didn't remove this for some reason)
2008-12-24
c
jfie
l
ds
Remove (merge didn'
t
r
e
move this
fo
r
s
o
me reason
)
commit
|
commitdiff
|
tree
2008-12-24
c
jfields
Remove
(
merge didn't remove this for some reason)
commit
|
commitdiff
|
tree
2008-12-22
cjfields
sync trunk with
b
ranch
commit
|
commitdiff
|
tree
2008-12-20
cjfield
s
5
.
6
.
1 is min perl version req
u
ired for all core module
s
now
commit
|
commitdiff
|
tree
2008-12-19
cjfields
u
p
d
a
te NAMES
commit
|
commitdiff
|
tree
2008-12-19
cj
f
ie
l
ds
sm
a
ll ty
p
o
commit
|
commitdiff
|
tree
2008-12-18
cjfields
typo
commit
|
commitdiff
|
tree
2008-12-18
cjfield
s
[b
u
g 27
1
4]
commit
|
commitdiff
|
tree
2008-12-17
cjfields
fix tes
t
numb
e
r
commit
|
commitdiff
|
tree
2008-12-17
cjfi
e
lds
update Te
s
t
::Warn (f
i
xes
Qual
.
t test problems with
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjfields
mi
s
sed one
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUtilities remote
t
ests back
o
n
line
(
simple tests only)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
EUtili
t
ies remot
e
tests back online
(
simple t
e
sts o
n
ly)
commit
|
commitdiff
|
tree
2008-12-16
cjfields
You
m
u
s
t
a
ctually test data if you want t
h
is module
.
.
.
commit
|
commitdiff
|
tree
2008-12-16
cjfiel
d
s
Don't use print! Ch
a
nging to $
s
elf->debug
or co
m
men
t
i
n
g out
commit
|
commitdiff
|
tree
2008-12-16
cjf
i
elds
Bio::G
r
ap
h
dep
r
ecat
e
d in 1
.
6
commit
|
commitdiff
|
tree
2008-12-16
cj
f
ields
stifle warnings when
passing string instead of in
t
eger
commit
|
commitdiff
|
tree
2008-12-16
cjfields
hash ref, not array ref
commit
|
commitdiff
|
tree
2008-12-16
c
j
fields
[bu
g
2637]
commit
|
commitdiff
|
tree
2008-12-16
cjfields
[
b
ug 2637]
commit
|
commitdiff
|
tree
2008-12-16
c
j
fields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-16
cj
f
i
elds
[
b
u
g
263
7
]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-15
cjfields
[
b
ug 2712]
commit
|
commitdiff
|
tree
2008-12-15
c
jfie
l
ds
scores
commit
|
commitdiff
|
tree
2008-12-15
c
jfields
remai
n
ing test
s
for Bio
:
:T
o
ol::EUtilities
commit
|
commitdiff
|
tree
2008-12-15
cjfields
mo
r
e test data
commit
|
commitdiff
|
tree
2008-12-15
cjfields
Updates:
commit
|
commitdiff
|
tree
2008-12-13
cjfield
s
initial batch o
f
EUtilP
a
rameters tes
t
s
commit
|
commitdiff
|
tree
2008-12-13
cjfields
e
info t
e
sts
commit
|
commitdiff
|
tree
2008-12-12
c
jfi
e
l
d
s
some
E
Utilities
tests (
p
arsing
f
rom files)
commit
|
commitdiff
|
tree
2008-12-12
c
j
fie
l
ds
s
o
m
e
tes
t
da
t
a for
B
io::Tools:
:
E
Utilities
commit
|
commitdiff
|
tree
2008-12-12
c
jf
i
elds
updates to E
U
tilities (getting ready for docs, tests
.
.
.
commit
|
commitdiff
|
tree
2008-12-12
c
j
fields
Move EUt
i
lParameters to Tools (seems
m
ore ap
p
rop
r
iate)
commit
|
commitdiff
|
tree
2008-12-11
cjfiel
d
s
fix for bu
g
when ge
t
tin
g
cache
d
response wi
t
h filen
a
me
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
small pointe
r
to
wiki pa
g
e (will update a
l
o
ng with
.
.
.
commit
|
commitdiff
|
tree
2008-12-11
cjfields
small update
commit
|
commitdiff
|
tree
2008-12-11
cjfields
upd
a
tes
commit
|
commitdiff
|
tree
2008-12-11
c
jfields
r
eturn, no
t
'return u
n
def'
commit
|
commitdiff
|
tree
2008-12-11
c
j
fields
r
eturn, not 're
t
urn und
e
f'
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bu
g
2
6
99]
commit
|
commitdiff
|
tree
2008-12-11
cjfields
[bug 269
9
]
commit
|
commitdiff
|
tree
2008-12-11
cjfi
e
ld
s
[bug 2707]
commit
|
commitdiff
|
tree
2008-12-10
cjfields
Removing from HEAD (d
e
preca
t
ed for 1
.
6)
commit
|
commitdiff
|
tree
2008-12-10
c
jfields
mini pod fi
x
commit
|
commitdiff
|
tree
2008-12-10
cjfields
update depr
e
cation list
commit
|
commitdiff
|
tree
2008-12-10
cjfields
remov
e
Bio::Graphics (se
p
arate
package now)
commit
|
commitdiff
|
tree
2008-12-10
cjf
i
elds
[bug 2637]
commit
|
commitdiff
|
tree
2008-12-10
cjf
i
elds
Rem
o
ve dependenci
e
s for Bio::Gr
a
p
hi
c
s and deprecat
e
d
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Squash
w
arning
commit
|
commitdiff
|
tree
2008-12-09
c
j
fields
diag(
)
only o
n
ver
b
ose
commit
|
commitdiff
|
tree
2008-12-09
cjfields
F
i
x last loop te
s
ts, mo
v
e s
o
me to can_
o
k
commit
|
commitdiff
|
tree
2008-12-09
cjfields
Modif
y
t
o te
s
t ne
w
temp classes and
e
nsure
t
h
at
a
dded
.
.
.
commit
|
commitdiff
|
tree
2008-12-09
cjfields
update Mauricio's email
commit
|
commitdiff
|
tree
2008-12-08
cjfiel
d
s
Upd
a
te Roy's email
commit
|
commitdiff
|
tree
2008-12-08
cj
f
i
e
l
d
s
Roy's ema
i
l (and bio
p
erl
.
org not b
i
ope
r
l
.
edu)
commit
|
commitdiff
|
tree
2008-12-08
cjfiel
d
s
U
pdate
d
emails
commit
|
commitdiff
|
tree
2008-12-07
cjf
i
elds
[bug 2699]
commit
|
commitdiff
|
tree
2008-12-05
cj
f
ie
l
ds
Need to retrieve the tree for outpu
t
commit
|
commitdiff
|
tree
2008-12-05
cjfields
[
b
u
g
2
4
50]
commit
|
commitdiff
|
tree
2008-12-04
cjfield
s
M
ake
T
ar
g
e
t
a
true DBLink
commit
|
commitdiff
|
tree
2008-12-04
cjfie
l
ds
Direct
o
ry is no longer need
e
d (
H
e
i
kki split t
h
is up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
add force_nse
t
e
sts
commit
|
commitdiff
|
tree
2008-12-03
cjfields
leave ID undefined if
i
t
isn't p
r
ese
n
t, but allow the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
Re
m
ove files a
c
c
ident
l
y
a
dded fr
o
m
last comm
i
t
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
Reorganize T
o
ols tests
(
needs some
m
ore splitting
)
commit
|
commitdiff
|
tree
2008-12-03
c
j
fi
e
ld
s
Remove
(tests are redundant, in Consed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
c
j
fields
Merge tests and remove redundant file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Up
d
ate test count
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
Mer
g
e
t
e
st
s
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remo
v
e
r
edundant fil
e
commit
|
commitdiff
|
tree
2008-12-03
c
j
fields
Rem
o
v
e old fil
e
s
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
S
tart Tool
s
move
commit
|
commitdiff
|
tree
2008-12-03
cjfields
small updates
:
commit
|
commitdiff
|
tree
2008-12-03
cjfields
for
g
ot to increment
t
est
count
commit
|
commitdiff
|
tree
2008-12-03
c
j
fields
A
dd a coup
l
e
o
f
tests f
o
r
s
e
q
_
id
(smal
l
but
significa
n
t
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
c
j
fields
[bu
g
2
45
0
]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[b
u
g 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 245
0
]
commit
|
commitdiff
|
tree
2008-12-02
c
j
fields
[bu
g
2
4
50]
commit
|
commitdiff
|
tree
2008-12-02
c
j
f
i
elds
s
o
me pod up
d
at
e
s
commit
|
commitdiff
|
tree
2008-12-02
c
jfiel
d
s
[
bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
fix erroneously renamed st
o
ckholm tes
t
s
commit
|
commitdiff
|
tree
2008-12-02
cjfields
small p
o
d fix
commit
|
commitdiff
|
tree
2008-11-30
cj
f
ields
sile
n
ce GuessSeqFormat
.
t warnings (not sure if old
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
c
jfields
r
earrange to avoid un
n
e
c
e
ssary warnings
commit
|
commitdiff
|
tree
2008-11-28
cjfields
A
d
d
warn
i
ng f
o
r missing
d
ata (
r
eal bug)
commit
|
commitdiff
|
tree
2008-11-28
cjfiel
d
s
hash ref, not a hash
commit
|
commitdiff
|
tree
2008-11-28
cjfields
te
s
t fil
e
name and test # correct
i
on
commit
|
commitdiff
|
tree
2008-11-28
c
jfie
l
ds
correc
t
t
est
file name
commit
|
commitdiff
|
tree
2008-11-28
cjfields
'::', not ':'
commit
|
commitdiff
|
tree
2008-11-28
cjfields
rename (re
c
u
r
s
ive tes
t
s think this is
a
test fi
l
e
)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
recurse into test subdirecto
r
ies (means any non-tes
t
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfields
remove redunda
n
t
c
opy
commit
|
commitdiff
|
tree
2008-11-28
cjfields
move into direct
o
ry structure
commit
|
commitdiff
|
tree
2008-11-28
cjfields
move into directo
r
y
s
tructur
e
(Da
v
eM++)
commit
|
commitdiff
|
tree
2008-11-26
cjfield
s
[bug 2567]
commit
|
commitdiff
|
tree
2008-11-26
cjfi
e
lds
Redu
n
dant;
fil
e
was renamed SearchIO_blast_pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cj
f
i
e
lds
[
b
u
g
2686]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
f
i
x s
u
bversion t
a
gs
commit
|
commitdiff
|
tree
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