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allow other SearchIO formats and parameters (though axt and sim4 are not working...
2010-11-05
Chri
s
F
i
e
lds
allo
w
other
S
earch
I
O form
a
ts a
n
d par
a
m
et
e
rs
(
though
.
.
.
commit
|
commitdiff
|
tree
2010-11-05
Chr
i
s
F
i
e
lds
t
e
s
t
s
f
or regions, requ
i
r
e
a
.
2
bit databas
e
so on
l
y
.
.
.
commit
|
commitdiff
|
tree
2010-11-05
Chris Fields
add an upp
e
rcase alias f
o
r db, test
s
pa
s
s
commit
|
commitdiff
|
tree
2010-11-05
Chri
s
Fiel
d
s
init
i
al ch
e
ckin of revamped
B
lat wrapper
commit
|
commitdiff
|
tree
2010-08-05
Chris Fields
[bug 2987]
r
emove warning (p
a
tch c
o
ur
t
esy
A
d
am Witn
e
y
commit
|
commitdiff
|
tree
2010-07-23
Chr
i
s Fields
Revert "add d
o
ts param"
commit
|
commitdiff
|
tree
2010-07-23
Chris Fields
add
d
o
t
s
p
aram
commit
|
commitdiff
|
tree
2010-07-23
Chris F
i
elds
[
R
T 58464] patching to
allow
file names
w
i
th spa
c
e
s
commit
|
commitdiff
|
tree
2010-07-05
Chris Fields
small fixes, but the previous code does work whe
n
setti
n
g
.
.
.
commit
|
commitdiff
|
tree
2010-07-04
Chris Fi
e
lds
spel
l
i
ng
commit
|
commitdiff
|
tree
2010-07-01
Chris Fields
move t
e
sts over
t
o tempfil
e
use
(tmpdir not
being cleaned up)
commit
|
commitdiff
|
tree
2010-07-01
Chris Fields
m
ove
to tempfiles for cl
e
anup
commit
|
commitdiff
|
tree
2010-07-01
Chr
i
s Fields
algorit
h
m
c
an
be SSEARCH as wel
l
; use test
_
output_file
.
.
.
commit
|
commitdiff
|
tree
2010-07-01
Chris
F
ields
c
ontigs off with Ubuntu pack
a
ged MAQ
commit
|
commitdiff
|
tree
2010-06-30
Chris Fiel
d
s
no_
s
equences -> num_sequences
commit
|
commitdiff
|
tree
2010-06-30
Ch
r
is
Fie
l
ds
some
t
weaks to get rid of warnings
commit
|
commitdiff
|
tree
2010-06-30
Chris Fields
m
or
e
r
obust
c
all to ulimit
commit
|
commitdiff
|
tree
2010-06-30
C
hris F
i
el
d
s
is(), not o
k
(
)
commit
|
commitdiff
|
tree
2010-06-30
Chris F
i
elds
skip i
f
version greater than 1
.
2
(old pr
i
m
e
r3 code)
commit
|
commitdiff
|
tree
2010-06-30
Chris Fields
add version() (backport from primer
3
r
e
du
x
)
commit
|
commitdiff
|
tree
2010-06-30
C
h
r
i
s
F
i
e
lds
align left
commit
|
commitdiff
|
tree
2010-06-30
C
hris
F
ield
s
fix
odd verb
o
sit
y
-de
p
e
ndent bug wit
h
EMBOSS
t
ests
commit
|
commitdiff
|
tree
2010-06-30
Chris Fields
a
d
d
m
i
nimal gitignore
commit
|
commitdiff
|
tree
2010-06-30
Chris Fi
e
ld
s
a
d
d ulimit -n check
,
as
these tes
t
s
fai
l
f
r
om too
ma
n
y
.
.
.
commit
|
commitdiff
|
tree
2010-06-30
Chris Fi
e
lds
add email
commit
|
commitdiff
|
tree
2010-06-30
Chr
i
s
F
i
elds
c
orrect skipped
n
umber of
t
ests
commit
|
commitdiff
|
tree
2010-06-30
Chris Fields
s
k
ip te
s
t count off, fixed
commit
|
commitdiff
|
tree
2010-06-30
Chris Fiel
d
s
Merge
branch 'mast
e
r' of githu
b
.
com:
b
ioperl/bi
o
p
erl-run
commit
|
commitdiff
|
tree
2010-06-06
C
h
ris
F
ields
a
dd default manifest
commit
|
commitdiff
|
tree