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biopet.biopet
Commits
f483b2e5
Commit
f483b2e5
authored
Oct 12, 2016
by
Sander Bollen
Browse files
version in rscript for cn mops
parent
2571243a
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R
View file @
f483b2e5
#!/usr/bin/env Rscript
suppressPackageStartupMessages
(
library
(
'cn.mops'
))
suppressPackageStartupMessages
(
library
(
'optparse'
))
suppressWarnings
(
suppressPackageStartupMessages
(
library
(
'cn.mops'
))
)
suppressWarnings
(
suppressPackageStartupMessages
(
library
(
'optparse'
))
)
# Script from https://git.lumc.nl/lgtc-bioinformatics/gapss3/blob/master/src/CNV/makeCnmops.sh
# modified to take arguments
...
...
@@ -11,7 +11,8 @@ option_list <- list(
make_option
(
c
(
"--cnr"
),
dest
=
"cnr"
),
make_option
(
c
(
"--chr"
),
dest
=
"chr"
),
make_option
(
c
(
"--threads"
),
dest
=
"threads"
,
default
=
8
,
type
=
"integer"
),
make_option
(
c
(
"--wl"
),
dest
=
"wl"
,
default
=
1000
,
type
=
"integer"
)
make_option
(
c
(
"--wl"
),
dest
=
"wl"
,
default
=
1000
,
type
=
"integer"
),
make_option
(
c
(
"--version"
),
action
=
"store_true"
,
default
=
FALSE
)
)
parser
<-
OptionParser
(
usage
=
"%prog [options] file"
,
option_list
=
option_list
)
...
...
@@ -19,6 +20,11 @@ arguments = parse_args(parser, positional_arguments=TRUE)
opt
=
arguments
$
options
args
=
arguments
$
args
if
(
opt
$
version
)
{
cat
(
toString
(
packageVersion
(
'cn.mops'
)))
quit
(
"no"
)
}
chromosome
<-
opt
$
chr
CNVoutput
<-
opt
$
cnv
CNRoutput
<-
opt
$
cnr
...
...
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