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
7594b89f
Commit
7594b89f
authored
May 02, 2016
by
Peter van 't Hof
Browse files
Fixed compile error
parent
6cbf2b4a
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
7594b89f
...
...
@@ -402,7 +402,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
if
(
out
!=
null
&&
!
org
.
broadinstitute
.
gatk
.
utils
.
io
.
IOUtils
.
isSpecialFile
(
out
))
outputFiles
:+=
VcfUtils
.
getVcfIndexFile
(
out
)
dbsnp
.
foreach
(
deps
:+=
VcfUtils
.
getVcfIndexFile
(
_
))
deps
++=
comp
.
filter
(
orig
=>
orig
!=
null
&&
(!
orig
.
getName
.
endsWith
(
".list"
))).
map
(
orig
=>
orig
+
".idx"
)
deps
++=
comp
.
filter
(
orig
=>
orig
!=
null
&&
(!
orig
.
getName
.
endsWith
(
".list"
))).
map
(
orig
=>
new
File
(
orig
+
".idx"
)
)
if
(
bamOutput
!=
null
&&
!
org
.
broadinstitute
.
gatk
.
utils
.
io
.
IOUtils
.
isSpecialFile
(
bamOutput
))
if
(!
disable_bam_indexing
)
outputFiles
:+=
new
File
(
bamOutput
.
getPath
.
stripSuffix
(
".bam"
)
+
".bai"
)
...
...
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