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Merge branch 'master' of git://github.com/fschwach/bioperl-live into topic/pull_request33
2013-08-09
Chri
s
Fields
M
erge branch 'mast
e
r
'
of git:
/
/github
.
com/fschwach
.
.
.
commit
|
commitdiff
|
tree
2013-08-09
C
hris
F
ields
Merge b
r
anch 'topi
c
/pull_reques
t
47_adsj'
commit
|
commitdiff
|
tree
2013-08-09
Ch
r
is Fie
l
ds
Merge bra
n
ch 'master' of git://github
.
c
om
/
adsj/biope
r
l
.
.
.
commit
|
commitdiff
|
tree
2013-08-09
Ch
r
is Fields
Merge branch
'
bugfix-exonerat
e
' of git://github
.
com
.
.
.
commit
|
commitdiff
|
tree
2013-08-09
C
h
ris Fields
Mer
g
e branch 'master
'
of g
i
t
:
//githu
b
.
com/viklund/bioperl
.
.
.
commit
|
commitdiff
|
tree
2013-05-21
C
h
r
i
s Fields
update tests
f
o
r perl 5
.
18
commit
|
commitdiff
|
tree
2013-02-20
Chris
Fields
Mer
g
e
branch 'm
a
ster' of github
.
com:bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2013-02-19
C
hris Fields
Merge
branch 'v1'
commit
|
commitdiff
|
tree
2013-02-19
C
hris Fields
Merge branc
h
'
v
1'
commit
|
commitdiff
|
tree
2012-10-01
Chris Fi
e
lds
squash a
c
oupl
e
of warni
n
gs with
m
ore
r
ecent versions
.
.
.
commit
|
commitdiff
|
tree
2012-07-26
Ch
r
is
F
ields
me
r
g
e
Peter's changes
i
n
commit
|
commitdiff
|
tree
2012-07-09
Chris Fie
l
ds
Merge
b
r
a
nch 'topic/eutils
-
m
igration'
commit
|
commitdiff
|
tree
2012-05-26
Ch
r
i
s Fields
Mer
g
e pull req
u
est
#
34 fro
m
T
ristanLefebure/codonbs
commit
|
commitdiff
|
tree
2012-01-21
Chris
Fields
Merge pull request
#
32
from fschwach/master
commit
|
commitdiff
|
tree
2012-01-13
Chris Fields
Mer
g
e pull reques
t
#31 from fs
c
hwac
h
/master
commit
|
commitdiff
|
tree
2011-12-09
Chris Fields
Merg
e
pull request
#
2
9
from
wkretzsch/
m
aster
commit
|
commitdiff
|
tree
2011-12-09
Chris Fields
Me
r
ge branch 'master' of htt
p
s://gi
t
hu
b
.
com
/
fgvieira
.
.
.
commit
|
commitdiff
|
tree
2011-11-29
C
hris Fie
l
ds
Merge branch 'embl_write_id_line_
f
ix'
commit
|
commitdiff
|
tree
2011-10-28
C
h
ris Field
s
Merge pul
l
r
equest #26 from fgvieira/master
commit
|
commitdiff
|
tree
2011-10-24
Chris
F
ields
Merg
e
b
ranc
h
'maste
r
'
of githu
b
.
com:bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2011-09-29
Ch
r
is Fields
M
erge branch
'
m
as
t
er'
of github
.
com:bi
o
perl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
Chri
s
F
i
eld
s
Merge pull req
u
est #
2
4
from carand
r
aug/bp_genbank_ref_ext
r
actor
commit
|
commitdiff
|
tree
2011-07-26
Ch
r
is Fields
Me
r
ge pull request #19
f
r
o
m
c
arandra
u
g/scri
p
t/extract_fe
a
tu
r
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Chris
Fie
l
ds
M
erge pull request
#18 from caran
d
raug/script/
p
erl
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Chris F
i
el
d
s
M
e
rge pull reques
t
#17 from
c
a
r
andrau
g
/m
a
ster
commit
|
commitdiff
|
tree
2011-06-20
C
hris Field
s
Me
r
ge pull req
u
est
#16 from cha
d
a
d
a
vis/
m
aster
commit
|
commitdiff
|
tree
2011-06-02
Chr
i
s Fields
Me
r
ge p
u
ll
re
q
u
e
st #15 f
r
om tupinek/master
commit
|
commitdiff
|
tree
2011-05-10
Chris Fiel
d
s
fix spelling
e
rrors, fixes
#
3
228
commit
|
commitdiff
|
tree
2011-04-13
Chris
F
ields
fix
skip test count (off by 1)
commit
|
commitdiff
|
tree
2011-04-13
Chris Fields
Mer
g
e branch 'topic/b
u
g_3196', fixes #3196 but needs
.
.
.
commit
|
commitdiff
|
tree
2011-04-13
Chris Fields
M
e
rge remote branch
'
wkretzs
c
h
/master'
commit
|
commitdiff
|
tree
2011-02-14
Chris Fie
l
ds
M
erge branch 'master' of github
.
com:bioperl/b
i
oper
l
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
Ch
r
is
Fiel
d
s
Merge branch 'topic/gj
u
ggle
r
_t
r
ee_fixes'
commit
|
commitdiff
|
tree
2010-11-08
Chris Fie
l
ds
Merge
b
ranch 'mas
t
er' of h
t
tps://github
.
com/gjug
g
l
er
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Chris
F
ields
M
e
rg
e
b
ra
n
c
h
'c
i
rcular'
commit
|
commitdiff
|
tree
2010-07-29
R
o
b
ert Buels
strip
key
w
o
rd
substitution fro
m
perl module
s
commit
|
commitdiff
|
tree
2010-07-23
Chris
Fi
e
lds
[RT 58464] patc
h
i
n
g
t
o
all
o
w file names wi
t
h sp
a
ces
commit
|
commitdiff
|
tree
2010-07-23
Chris Fields
Merge branc
h
'topic/cjfiel
d
s
_
interpro_
g
et_dbxref
'
commit
|
commitdiff
|
tree
2010-07-03
Chris Fiel
d
s
Merge branch 'topic
/
species_proxy'
commit
|
commitdiff
|
tree
2010-06-29
Chris Fields
Merge branch
'
ma
s
te
r
' in
t
o to
p
i
c
/spec
i
es
_
prox
y
commit
|
commitdiff
|
tree
2010-06-22
Ch
r
is Fields
fix conflict
commit
|
commitdiff
|
tree
2010-06-10
Chr
i
s F
i
e
l
ds
Ben's c
h
a
n
ges
to fix bug with file, along with comme
n
t
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
C
h
ris Fiel
d
s
Merge bra
n
ch 'to
p
ic/bug3
0
89'
commit
|
commitdiff
|
tree
2010-06-06
Ch
r
is Fields
Merg
e
B
r
ian'
s
branch
commit
|
commitdiff
|
tree
2010-06-04
C
hris Fields
M
e
rge branc
h
'
m
aster' of
github
.
com:bio
p
e
r
l
/bi
o
perl
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
Chr
i
s Fields
Merge
branch 'master'
of
github
.
c
om:bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
Chris
F
i
eld
s
can't looku
p
an
undef
i
ned value
as a
n
executable
commit
|
commitdiff
|
tree
2010-05-20
Chris Fields
Merge bran
c
h
'master' of github
.
com:bi
o
p
e
rl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
C
hris Fields
Merge branch 'mast
e
r'
o
f gi
t
hub
.
com:biope
r
l/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-17
C
h
ris
F
ields
Merge branch 'master' of git@
g
ithub
.
com:biope
r
l/bio
p
erl
.
.
.
commit
|
commitdiff
|
tree
2010-05-10
c
j
fields
m
a
ke test le
s
s prone to volatile
c
hanges
commit
|
commitdiff
|
tree
2010-03-06
cjfields
fix re
m
o
teblast parsing
(almost complete refacto
r
of
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
c
jfields
nex
t
, not redo
commit
|
commitdiff
|
tree
2010-03-04
cjfields
Add a fini
t
e num
b
er
o
f a
t
te
m
pts
f
or
r
e
p
ort retr
i
eval
commit
|
commitdiff
|
tree
2010-03-04
cjfields
remot
e
BLAST is timing out when usi
n
g CDD and r
p
sbl
a
st
commit
|
commitdiff
|
tree
2009-11-25
cjfields
add n param
e
ter
(
not
t
e
sted) courtes
y
Nevo B
a
nd (not
.
.
.
commit
|
commitdiff
|
tree
2009-09-16
cjfi
e
lds
[
cage clea
n
ing]
commit
|
commitdiff
|
tree
2009-07-03
c
j
fie
l
d
s
catch edge cases where w
e
uninten
t
ionally pass an undef
.
.
.
commit
|
commitdiff
|
tree
2009-05-04
cjfields
minor formatting fix
commit
|
commitdiff
|
tree
2009-02-23
cjfields
first pass at a K
o
mo
d
o BioPerl template file
commit
|
commitdiff
|
tree
2009-01-15
cjfields
Don'
t
qu
o
t
e
meta i
f
u
sing Windows
commit
|
commitdiff
|
tree
2008-12-20
cjf
i
elds
re
m
ove BPli
t
e tests completely
commit
|
commitdiff
|
tree
2008-12-20
cjfields
Remove BPlite from us
e
commit
|
commitdiff
|
tree
2008-12-11
cjfie
l
d
s
[
bug 2707]
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Reorga
n
ize Tools te
s
t
s
(needs some more splitting)
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ield
s
m
o
ve i
n
to directory s
t
r
u
cture
commit
|
commitdiff
|
tree
2008-11-25
cjf
i
elds
po,
n
ot
p
oa
commit
|
commitdiff
|
tree
2008-11-25
cjfields
s
p
lit
u
p
A
l
ignIO
t
ests
commit
|
commitdiff
|
tree
2008-11-17
cjfields
[tests]
commit
|
commitdiff
|
tree
2008-02-11
c
j
fie
l
ds
remove
c
o
m
m
e
nt (
m
ake sur
e
tempfi
l
e/tempdirs stored
.
.
.
commit
|
commitdiff
|
tree
2008-02-11
cjfields
Fix for
b
ug 24
1
3
.
S
houldn't we delegate
a
ll
I
O-related
.
.
.
commit
|
commitdiff
|
tree
2007-10-23
cjfields
bug
2367
commit
|
commitdiff
|
tree
2007-07-06
c
j
fields
M
u
s
t
a
llow other S
e
arc
h
IO readmethod
s
(anythin
g
t
hat
.
.
.
commit
|
commitdiff
|
tree
2007-01-19
c
jfields
change
F
ile::Path verbosity to
only be TR
U
E w
h
en debug
g
ing
commit
|
commitdiff
|
tree
2007-01-18
c
jfields
re
m
ove
c
omments; cleanup() should now w
o
rk (fingers
.
.
.
commit
|
commitdiff
|
tree
2007-01-18
cjfields
r
evert b
a
ck t
o
normal f
r
om
d
e
b
ugging
commit
|
commitdiff
|
tree
2007-01-18
cjfields
Bug 2183
commit
|
commitdiff
|
tree