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Merge pull request #15 from tupinek/master
2011-06-02
C
hris Fields
Merge pull reque
s
t #15
from tu
p
in
e
k/master
commit
|
commitdiff
|
tree
2011-05-10
Chris
Field
s
fix spellin
g
errors, f
i
xes #3228
commit
|
commitdiff
|
tree
2011-04-13
Chris
F
ields
fix s
k
ip t
e
st co
u
nt (off
by
1)
commit
|
commitdiff
|
tree
2011-04-13
C
h
ris Fields
Merge br
a
nch 't
o
p
i
c/b
u
g
_
3196', fixes #31
9
6 but
n
eeds
.
.
.
commit
|
commitdiff
|
tree
2011-04-13
Chris Fields
Mer
g
e
remote branch 'wkretzsch/master'
commit
|
commitdiff
|
tree
2011-02-14
Chr
i
s Fi
e
l
ds
Merge branch '
m
aster'
of g
i
t
hub
.
c
om:bioperl/bi
o
perl
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
Chris Fields
Merge
branch '
t
opic/gjuggler_tree_fixes'
commit
|
commitdiff
|
tree
2010-11-08
Chris Fields
Merge branch 'master' of
https://g
i
thu
b
.
com/g
j
uggler
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Chr
i
s
Fields
Merge bran
c
h
'cir
c
ular'
commit
|
commitdiff
|
tree
2010-07-29
Rober
t
Buel
s
s
t
rip
k
eyword su
b
stituti
o
n from
perl
modu
l
es
commit
|
commitdiff
|
tree
2010-07-23
Chris Fields
[RT 58464
]
patching to allow fi
l
e names
w
ith spaces
commit
|
commitdiff
|
tree
2010-07-23
C
h
ris Field
s
M
e
rge
branch
'topic/
c
jfields_
i
nterpro_get_dbxre
f
'
commit
|
commitdiff
|
tree
2010-07-03
C
h
r
is F
i
e
l
d
s
M
erge bran
c
h 'topic/species_proxy'
commit
|
commitdiff
|
tree
2010-06-29
C
hri
s
Fields
Merge branch 'm
a
st
e
r' into
t
opic/spec
i
e
s
_proxy
commit
|
commitdiff
|
tree
2010-06-22
Chris Fields
fi
x
conflict
commit
|
commitdiff
|
tree
2010-06-10
C
h
r
is Fields
B
e
n
's
c
hanges to fix b
u
g
w
ith file,
a
long with c
o
m
ment
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Chris Fields
Merge branch 'topi
c
/bug3089
'
commit
|
commitdiff
|
tree
2010-06-06
Chris Fields
M
e
rge Brian's
b
ran
c
h
commit
|
commitdiff
|
tree
2010-06-04
Chris Fields
Merge branc
h
'master' of github
.
com:
b
ioperl/bio
p
er
l
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
Chr
i
s Fi
e
ld
s
Mer
g
e br
a
n
c
h '
m
aster' of github
.
com:bio
p
erl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
Chris Fields
can
'
t
l
ookup an
u
ndefined valu
e
a
s an executable
commit
|
commitdiff
|
tree
2010-05-20
Chri
s
F
ields
Merge bran
c
h 'mast
e
r' of g
i
thub
.
com:bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
Chris
F
ields
Merge branch 'ma
s
te
r
'
o
f github
.
com:
b
i
o
perl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-17
Chr
i
s Fields
Merge
b
r
an
c
h 'ma
s
ter' of
g
it@githu
b
.
com:bio
p
e
rl/biop
e
r
l
.
.
.
commit
|
commitdiff
|
tree
2010-05-10
cj
f
ields
make test less p
r
o
n
e to volatile changes
commit
|
commitdiff
|
tree
2010-03-06
cjfields
f
ix remotebl
a
st pars
i
ng (almost complete refactor of
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
cjfields
nex
t
, not redo
commit
|
commitdiff
|
tree
2010-03-04
cjfields
Add a
finite nu
m
b
e
r of
a
ttempts for r
e
port retrieval
commit
|
commitdiff
|
tree
2010-03-04
cjfields
re
m
ote BLAST
i
s t
i
ming out when u
s
i
ng CDD and rpsblast
commit
|
commitdiff
|
tree
2009-11-25
cjf
i
elds
add n parameter
(
not te
s
ted) cou
r
tesy Nevo Band (not
.
.
.
commit
|
commitdiff
|
tree
2009-09-16
cjf
i
el
d
s
[cage cleaning]
commit
|
commitdiff
|
tree
2009-07-03
cj
f
ields
catch e
d
g
e cases where we unintentionally pass
a
n un
d
ef
.
.
.
commit
|
commitdiff
|
tree
2009-05-04
cjfields
minor forma
t
ting fix
commit
|
commitdiff
|
tree
2009-02-23
cjfie
l
ds
first pass at a Komodo
B
ioPerl
t
emplate file
commit
|
commitdiff
|
tree
2009-01-15
c
j
f
ields
Don'
t
quotemeta if using Win
d
ows
commit
|
commitdiff
|
tree
2008-12-20
cjfi
e
lds
remove BPlite
t
ests
c
omp
l
etely
commit
|
commitdiff
|
tree
2008-12-20
cjfields
R
emove BPlite from u
s
e
commit
|
commitdiff
|
tree
2008-12-11
c
j
f
i
e
l
ds
[bug 27
0
7]
commit
|
commitdiff
|
tree
2008-12-03
cj
f
i
e
l
ds
Reo
r
ganize
T
ools
t
ests (needs so
m
e more splitting)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
m
o
v
e
in
t
o directory structur
e
commit
|
commitdiff
|
tree
2008-11-25
cjfields
po, not p
o
a
commit
|
commitdiff
|
tree
2008-11-25
c
j
fiel
d
s
split u
p
AlignI
O
tests
commit
|
commitdiff
|
tree
2008-11-17
cj
f
ield
s
[test
s
]
commit
|
commitdiff
|
tree
2008-02-11
cjfields
remove commen
t
(make sure tempfile/te
m
pd
i
rs st
o
red
.
.
.
commit
|
commitdiff
|
tree
2008-02-11
cjfields
Fix
f
or bug 2413
.
S
houldn't we
delegate all IO-rela
t
ed
.
.
.
commit
|
commitdiff
|
tree
2007-10-23
c
j
fields
bug 2367
commit
|
commitdiff
|
tree
2007-07-06
c
jfields
Must all
o
w o
t
her
S
earchIO readmethods (any
t
hing
t
h
a
t
.
.
.
commit
|
commitdiff
|
tree
2007-01-19
cjfields
change File::
P
ath verbosity to
on
l
y be TRU
E
when debugging
commit
|
commitdiff
|
tree
2007-01-18
c
j
fields
remove co
m
me
n
t
s; cleanup
(
) shou
l
d now work (finge
r
s
.
.
.
commit
|
commitdiff
|
tree
2007-01-18
cjfield
s
revert back to
normal from d
e
b
u
gging
commit
|
commitdiff
|
tree
2007-01-18
cjfields
Bu
g
2183
commit
|
commitdiff
|
tree