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Roy's email (and bioperl.org not bioperl.edu)
2008-12-08
cjfi
e
lds
Roy'
s
email (
a
nd
b
iop
e
rl
.
org not bioperl
.
edu)
commit
|
commitdiff
|
tree
2008-12-08
cjfields
U
p
dated e
m
ails
commit
|
commitdiff
|
tree
2008-12-07
cjf
i
e
l
ds
[
b
u
g
2699]
commit
|
commitdiff
|
tree
2008-12-05
cjfields
Nee
d
to
r
etrieve the tree for ou
t
p
u
t
commit
|
commitdiff
|
tree
2008-12-05
cjf
i
elds
[b
u
g 2
4
5
0
]
commit
|
commitdiff
|
tree
2008-12-04
cjfield
s
Make Tar
g
et a true DBLink
commit
|
commitdiff
|
tree
2008-12-04
cjf
i
el
d
s
Di
r
ectory is no longer needed (Heikki split this up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
add force_ns
e
tests
commit
|
commitdiff
|
tree
2008-12-03
cjfields
leave ID undefined if it isn't
pr
e
sent, but
all
o
w
t
he
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove files accidently added f
r
o
m last c
o
mm
i
t
commit
|
commitdiff
|
tree
2008-12-03
c
j
fiel
d
s
Reorganize Tools tests (
n
e
eds some more s
p
lit
t
ing
)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
R
e
m
o
v
e (t
e
sts are
r
edu
n
dant, in C
o
nsed
.
t
)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge tests and
r
emove redundant file
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Update test count
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
d
s
Merge tes
t
s
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
d
s
Remove re
d
unda
n
t file
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
R
e
m
o
ve old files
commit
|
commitdiff
|
tree
2008-12-03
cjfields
S
tart To
o
ls move
commit
|
commitdiff
|
tree
2008-12-03
c
jfiel
d
s
small updates
:
commit
|
commitdiff
|
tree
2008-12-03
cjfields
for
g
ot
t
o increment test co
u
nt
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Add a couple of t
e
sts fo
r
seq_
i
d (small but significant
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[b
u
g
2450
]
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
lds
[bug 24
5
0]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[
b
ug 2
4
50]
commit
|
commitdiff
|
tree
2008-12-02
cjfiel
d
s
so
m
e pod updates
commit
|
commitdiff
|
tree
2008-12-02
cjfiel
d
s
[
b
ug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cj
f
i
e
lds
fix erron
e
ously renam
e
d stock
h
o
l
m tests
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
lds
small p
o
d fix
commit
|
commitdiff
|
tree
2008-11-30
cjfiel
d
s
silence GuessS
e
q
F
ormat
.
t warnings
(
no
t
s
ure if old
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
c
j
f
i
e
lds
rearra
n
ge to avoid unne
c
es
s
ary wa
r
nings
commit
|
commitdiff
|
tree
2008-11-28
cjfields
A
d
d
warning for missing data (real bug
)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
hash ref, no
t
a hash
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ie
l
ds
test f
i
l
e
name and
test
# c
o
rrection
commit
|
commitdiff
|
tree
2008-11-28
c
j
f
i
elds
correct te
s
t file name
commit
|
commitdiff
|
tree
2008-11-28
cjf
i
elds
'::', no
t
'
:
'
commit
|
commitdiff
|
tree
2008-11-28
c
j
f
ield
s
r
ename (recursive test
s
th
i
nk this is
a test file)
commit
|
commitdiff
|
tree
2008-11-28
cjfie
l
d
s
recurse into t
e
st su
b
d
irectories
(
m
ea
n
s a
n
y non-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfi
e
l
d
s
rem
o
ve redunda
n
t copy
commit
|
commitdiff
|
tree
2008-11-28
cjfi
e
lds
move into dir
e
ctory structure
commit
|
commitdiff
|
tree
2008-11-28
cjfields
move into directory structure (DaveM
+
+)
commit
|
commitdiff
|
tree
2008-11-26
cjf
i
elds
[bu
g
2567]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
Redundan
t
; file w
a
s rename
d
SearchI
O
_blast
_
pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
c
jfields
[bug 2686]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
f
ix
s
ubversion tags
commit
|
commitdiff
|
tree
2008-11-25
cjfield
s
po, not poa
commit
|
commitdiff
|
tree
2008-11-25
cjfiel
d
s
fix undefined value warnings
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 26
8
6]
commit
|
commitdiff
|
tree
2008-11-25
cjfie
l
d
s
[bug 2641,
2
64
2
]
commit
|
commitdiff
|
tree
2008-11-25
cjfi
e
lds
s
plit
u
p AlignIO te
s
ts
commit
|
commitdiff
|
tree
2008-11-25
cjfi
e
lds
[bug
2
682]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 2
6
3
0
]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
ields
[bug
263
3
]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
ields
[bu
g
26
6
3]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[b
u
g 2
6
30]
commit
|
commitdiff
|
tree
2008-11-24
c
j
f
i
elds
[
bug 226
2
]
commit
|
commitdiff
|
tree
2008-11-24
cjfi
e
lds
[bug 26
3
0]
commit
|
commitdiff
|
tree
2008-11-18
cjf
i
elds
*
D
ouble-c
h
e
cke
d
data,
t
ested result
s
w
e
r
e wr
o
ng
commit
|
commitdiff
|
tree
2008-11-18
c
j
fields
* seq_
i
nds
is not defi
n
ed for Model-based
HSPs
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* fi
x
POD
commit
|
commitdiff
|
tree
2008-11-17
cj
f
ields
*
'highly'
(
and I g
e
t r15000!)
commit
|
commitdiff
|
tree
2008-11-17
cjfields
Remove redu
n
dant tes
t
f
iles
commit
|
commitdiff
|
tree
2008-11-17
c
jf
i
elds
[tests]
commit
|
commitdiff
|
tree
2008-11-17
c
j
fields
move r
e
su
l
ts2has
h
tes
t
uti
l
i
ty sub to
S
earchUtils
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[bug
2
663]
commit
|
commitdiff
|
tree
2008-11-16
cjfield
s
perl
t
idy
commit
|
commitdiff
|
tree
2008-11-16
cjfield
s
[b
u
g 2635]
commit
|
commitdiff
|
tree
2008-11-14
cjfields
[bug
2
656]
commit
|
commitdiff
|
tree
2008-11-11
c
j
fields
remove debugging l
i
n
e
s
commit
|
commitdiff
|
tree
2008-11-11
cjfields
remove fixed verbose flag
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bu
g
265
0
]
commit
|
commitdiff
|
tree
2008-11-11
cjf
i
e
l
ds
Clarify resul
t
_count (discussions on mail li
s
t per
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cjfields
[bug 2632
]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[bug 2645]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wra
p
t
e
xt
commit
|
commitdiff
|
tree
2008-11-04
cjfields
* parse
'
Feature
s
i
n
this
part of s
u
b
j
ec
t
sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
c
jfields
* parse 'Features in
t
his part of
s
ubject
s
eque
n
c
e
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bug 2632]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix seq_
i
nds()
;
wasn't calling identical res
i
dues for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjfields
[bug 2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfiel
d
s
[bug 263
0
]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
Fix un
l
ink()
w
ar
n
ing
commit
|
commitdiff
|
tree
2008-10-26
cjfields
end = start if only
start is
p
a
ssed
commit
|
commitdiff
|
tree
2008-10-26
cjfiel
d
s
u
se valid_Location to check
L
ocation sta
t
e
commit
|
commitdiff
|
tree
2008-10-26
cjfields
add docs for LocationI
m
ethod v
a
l
id
_
Locat
i
o
n
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
[bu
g
2621]
commit
|
commitdiff
|
tree
2008-10-26
cjfie
l
ds
[bug 2621
]
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
[bug 2624
]
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
[
b
ug
2
621]
commit
|
commitdiff
|
tree
2008-10-25
cjfields
bulle
t
-p
r
oof
p
rot
o
type
t
est
commit
|
commitdiff
|
tree
2008-10-22
c
jfields
fix
file properties
commit
|
commitdiff
|
tree
2008-10-22
cjfiel
d
s
new m
o
d
ule
f
or parsing vecscreen -f 3 output, c
o
urt
e
sy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cj
f
ield
s
a
dd -sour
c
e
for ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfi
e
l
ds
[bug 2563]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
typo
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-10
cjfields
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
c
j
fields
a
d
d svn tag
commit
|
commitdiff
|
tree
2008-10-07
cjfie
l
ds
T
ODO's work
commit
|
commitdiff
|
tree
next