Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
ceb905da
Commit
ceb905da
authored
Oct 06, 2016
by
Sander Bollen
Browse files
gracecully exit
parent
e0e20fa1
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R
View file @
ceb905da
...
...
@@ -26,7 +26,20 @@ windowLength <- opt$wl
bamFile
<-
args
BAMFiles
<-
strsplit
(
c
(
bamFile
),
" "
)[[
1
]]
bamDataRanges
<-
getReadCountsFromBAM
(
BAMFiles
,
mode
=
"paired"
,
refSeqName
=
chromosome
,
WL
=
windowLength
,
parallel
=
opt
$
threads
)
bamDataRanges
<-
tryCatch
(
{
getReadCountsFromBAM
(
BAMFiles
,
mode
=
"paired"
,
refSeqName
=
chromosome
,
WL
=
windowLength
,
parallel
=
opt
$
threads
)
},
error
=
function
(
e
)
{
quit
(
"no"
)
},
warning
=
function
(
w
)
{
quit
(
"no"
)
},
finally
=
{
}
)
write.table
(
as.data.frame
(
bamDataRanges
),
quote
=
FALSE
,
opt
$
rawoutput
,
row.names
=
FALSE
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment