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fix skip miscounts
2013-09-07
Chris Fields
f
ix sk
i
p miscoun
t
s
commit
|
commitdiff
|
tree
2013-09-02
Chris Fields
Merge b
r
anc
h
'
to
p
ic/
t
ravi
s
-scr
i
pt
s
'
commit
|
commitdiff
|
tree
2013-08-09
Chris Fi
e
lds
Mer
g
e branch 'm
a
s
t
e
r
'
of git://github
.
com/fschwach
.
.
.
commit
|
commitdiff
|
tree
2013-08-09
Chris Fields
Me
r
ge branch
'
topic/pul
l
_
reques
t
4
7
_adsj'
commit
|
commitdiff
|
tree
2013-08-09
Chris Fie
l
ds
M
erge br
a
nch 'mas
t
er' of
git://github
.
com/adsj/bioperl
.
.
.
commit
|
commitdiff
|
tree
2013-08-09
Chris Field
s
Merg
e
bra
n
ch '
b
ugfix-exonerate' of git://github
.
com
.
.
.
commit
|
commitdiff
|
tree
2013-08-09
Chris
Fields
Mer
g
e branc
h
'mas
t
e
r
' of
gi
t
://gi
t
hub
.
com/viklund/bioperl
.
.
.
commit
|
commitdiff
|
tree
2013-05-21
Chris Fields
update tests
f
or pe
r
l
5
.
18
commit
|
commitdiff
|
tree
2013-02-20
Chris Fields
Merg
e
br
a
nch 'master
'
of g
i
thu
b
.
com:
b
iop
e
rl/b
i
operl
.
.
.
commit
|
commitdiff
|
tree
2013-02-19
Ch
r
i
s
Fields
Merge
b
ranch
'
v1'
commit
|
commitdiff
|
tree
2013-02-19
Chris
F
ie
l
ds
M
e
rge branch 'v1'
commit
|
commitdiff
|
tree
2012-10-01
Chri
s
Fiel
d
s
squash a cou
p
le
of warnings with more recent versions
.
.
.
commit
|
commitdiff
|
tree
2012-07-26
Chri
s
Fi
e
l
ds
merge Peter's changes in
commit
|
commitdiff
|
tree
2012-07-09
Chri
s
Fields
Merge br
a
nch 'topi
c
/eutils-migration'
commit
|
commitdiff
|
tree
2012-05-26
Chris F
i
elds
Merge pu
l
l request #34 fr
o
m TristanLefebure
/
codonbs
commit
|
commitdiff
|
tree
2012-01-21
C
hri
s
Fields
M
erge pull request #32 fr
o
m fschwa
c
h/mast
e
r
commit
|
commitdiff
|
tree
2012-01-13
C
h
r
is Fields
M
erge pull
r
eq
u
est #
3
1 f
r
o
m fschwac
h
/master
commit
|
commitdiff
|
tree
2011-12-09
Chri
s
Fi
e
lds
Me
r
ge
p
ull
request
#29
f
r
om wkretzsch/m
a
ster
commit
|
commitdiff
|
tree
2011-12-09
C
h
ris Fields
Merge
branch
'
mast
e
r' of https://
g
i
t
h
ub
.
com/fgvi
e
ira
.
.
.
commit
|
commitdiff
|
tree
2011-11-29
Ch
r
i
s
F
i
elds
Merge
b
ranch 'embl_write_id_line_fix'
commit
|
commitdiff
|
tree
2011-10-28
Chris Fields
Merge pu
l
l re
q
uest #26
from fgv
i
eira/maste
r
commit
|
commitdiff
|
tree
2011-10-24
Chris
Fi
e
ld
s
M
erge br
a
nch 'master'
o
f githu
b
.
co
m
:bioperl
/
bioperl
.
.
.
commit
|
commitdiff
|
tree
2011-09-29
Chris Fie
l
ds
Merge b
r
a
n
c
h 'mast
e
r'
of githu
b
.
com
:
bioper
l
/bioperl
.
.
.
commit
|
commitdiff
|
tree
2011-09-22
Chris
F
ie
l
d
s
Merge pu
l
l request #2
4
from caran
d
r
a
ug/bp_genbank_ref_
e
xtractor
commit
|
commitdiff
|
tree
2011-07-26
Chris Fi
e
l
d
s
M
erge pull re
q
uest #1
9
from cara
n
dra
u
g/scr
i
p
t/extract_feat
u
r
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Chris
F
ields
Merge pull request #1
8
from c
a
r
a
ndr
a
ug/s
c
ript/
p
erl
.
.
.
commit
|
commitdiff
|
tree
2011-07-25
Chris Fields
Me
r
ge pull
re
q
uest #17 from ca
r
an
d
raug
/
master
commit
|
commitdiff
|
tree
2011-06-20
Chris
Fi
e
lds
Merge pul
l
r
eque
s
t #16 fr
o
m
c
h
adadavi
s
/
m
aster
commit
|
commitdiff
|
tree
2011-06-02
C
hris Fields
Merge pull request #15 from tupinek/ma
s
ter
commit
|
commitdiff
|
tree
2011-05-10
Chris Fields
fi
x
spelling errors, fixes #3228
commit
|
commitdiff
|
tree
2011-04-13
Chri
s
Fi
e
lds
fix sk
i
p
t
est count (of
f
b
y
1)
commit
|
commitdiff
|
tree
2011-04-13
Chris Fie
l
d
s
Merge branch 'topic
/
bug_
3
196', fixes
#3196 but ne
e
ds
.
.
.
commit
|
commitdiff
|
tree
2011-04-13
Chris Fields
M
erge remote branch
'
wkretzsch/maste
r
'
commit
|
commitdiff
|
tree
2011-02-14
Chri
s
Fiel
d
s
Merge branch 'master' of g
i
t
h
ub
.
c
o
m:b
i
operl/bi
o
perl
.
.
.
commit
|
commitdiff
|
tree
2010-11-09
C
h
r
is Fiel
d
s
M
e
rge branc
h
'
t
o
pic/gj
u
g
g
ler_tr
e
e_fixes'
commit
|
commitdiff
|
tree
2010-11-08
Chris Fields
Mer
g
e b
r
a
n
ch 'master' of
https://github
.
com/
g
juggler
.
.
.
commit
|
commitdiff
|
tree
2010-08-17
Chris Fields
Merg
e
branch 'circula
r
'
commit
|
commitdiff
|
tree
2010-07-29
Robert Buels
strip keyword substituti
o
n from
perl
m
odules
commit
|
commitdiff
|
tree
2010-07-23
Chris Fiel
d
s
[R
T
58464] patching to allow
file names w
i
th spac
e
s
commit
|
commitdiff
|
tree
2010-07-23
Chri
s
Fields
Merge branc
h
'
t
o
p
ic/cj
f
ields_
i
nterpro
_
get_dbxr
e
f'
commit
|
commitdiff
|
tree
2010-07-03
Chris Fi
e
ld
s
Merge
branch 'topi
c
/species_prox
y
'
commit
|
commitdiff
|
tree
2010-06-29
C
h
ris Field
s
Merge branch
'master' into topic/species_p
r
oxy
commit
|
commitdiff
|
tree
2010-06-22
Chris F
i
elds
fi
x
c
o
n
flict
commit
|
commitdiff
|
tree
2010-06-10
C
hris
Fields
B
en's changes to fix bug
with file, along
w
it
h
comment
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
C
hris Fields
Merge branch 'to
p
ic/b
u
g3089'
commit
|
commitdiff
|
tree
2010-06-06
Chri
s
Fields
Me
r
ge Brian's branch
commit
|
commitdiff
|
tree
2010-06-04
Chris Fields
M
erge branch '
m
a
ster' of github
.
com:bi
o
p
er
l
/bi
o
perl
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
Chris Fields
Me
r
ge
b
ranch
'
ma
s
ter'
o
f github
.
c
om:bioperl/b
i
operl
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
Chr
i
s
Fiel
d
s
c
an't lookup
a
n und
e
f
i
ned
value as an
e
x
ecutab
l
e
commit
|
commitdiff
|
tree
2010-05-20
Chris
Fields
Merge bran
c
h 'master' of g
i
thub
.
co
m
:bioperl/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-20
Chris
F
i
e
lds
Merge branch
'
master' of github
.
c
om:biope
r
l/
b
iope
r
l
.
.
.
commit
|
commitdiff
|
tree
2010-05-17
Chris Fields
Merge branch 'm
a
ster' o
f
git@g
i
th
u
b
.
com:biop
e
r
l
/bioperl
.
.
.
commit
|
commitdiff
|
tree
2010-05-10
cjfi
e
lds
m
a
ke test less p
r
one to volatile c
h
an
g
es
commit
|
commitdiff
|
tree
2010-03-06
cjf
i
e
l
ds
fix rem
o
tebl
a
s
t pars
i
ng (
a
lmo
s
t compl
e
t
e refactor of
.
.
.
commit
|
commitdiff
|
tree
2010-03-05
c
jfields
next, not redo
commit
|
commitdiff
|
tree
2010-03-04
cjfields
Add a
f
in
i
te number of attempts for report retrieval
commit
|
commitdiff
|
tree
2010-03-04
c
j
fields
remote BLAST
i
s timing out when u
s
ing C
D
D and
r
p
s
blast
commit
|
commitdiff
|
tree
2009-11-25
cjfields
add n
p
arameter (n
o
t t
e
sted) c
o
urtesy Nevo Band (not
.
.
.
commit
|
commitdiff
|
tree
2009-09-16
cjfield
s
[cage clean
i
ng]
commit
|
commitdiff
|
tree
2009-07-03
cjfi
e
lds
catch ed
g
e c
a
ses where we unintent
i
on
a
lly pass
a
n undef
.
.
.
commit
|
commitdiff
|
tree
2009-05-04
cjf
i
elds
minor formatti
n
g
fix
commit
|
commitdiff
|
tree
2009-02-23
cjfield
s
fir
s
t pass at a Komodo BioPerl template file
commit
|
commitdiff
|
tree
2009-01-15
cjfields
Don't quot
e
meta
if
using Windows
commit
|
commitdiff
|
tree
2008-12-20
cjfi
e
l
d
s
re
m
o
ve BPlite tests completely
commit
|
commitdiff
|
tree
2008-12-20
cjf
i
elds
Remove BPl
i
te fr
o
m use
commit
|
commitdiff
|
tree
2008-12-11
cj
f
i
e
lds
[bu
g
270
7
]
commit
|
commitdiff
|
tree
2008-12-03
cjfie
l
ds
Reorganize
T
o
ol
s
t
es
t
s (needs some more
sp
l
itting)
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
move into directory struc
t
ure
commit
|
commitdiff
|
tree
2008-11-25
c
j
fi
e
l
d
s
po
,
not poa
commit
|
commitdiff
|
tree
2008-11-25
cjfields
spli
t
up AlignIO tests
commit
|
commitdiff
|
tree
2008-11-17
cjfields
[tests]
commit
|
commitdiff
|
tree
2008-02-11
cjfields
remo
v
e comm
e
n
t
(make sure temp
f
ile/tempdirs stored
.
.
.
commit
|
commitdiff
|
tree
2008-02-11
cjfields
Fix for bug
2
413
.
Shouldn't we delegate all IO-
r
ela
t
e
d
.
.
.
commit
|
commitdiff
|
tree
2007-10-23
c
jfields
bug
2367
commit
|
commitdiff
|
tree
2007-07-06
cjfields
M
ust allow o
t
her Search
I
O r
e
admethods (anyth
i
ng
t
hat
.
.
.
commit
|
commitdiff
|
tree
2007-01-19
cjfields
change
F
ile::Path v
e
rbosity
to only be TRUE
w
hen deb
u
gging
commit
|
commitdiff
|
tree
2007-01-18
cjfie
l
d
s
remove comments; cleanu
p
()
s
hould now work (fing
e
rs
.
.
.
commit
|
commitdiff
|
tree
2007-01-18
cjfields
revert back to no
r
mal f
r
om debug
g
ing
commit
|
commitdiff
|
tree
2007-01-18
c
j
fields
Bug
2
183
commit
|
commitdiff
|
tree