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biopet.biopet
Commits
c1aee221
Commit
c1aee221
authored
Feb 23, 2015
by
Wai Yi Leung
Browse files
Fixing seqstat usage of outDir
parent
163386a3
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
View file @
c1aee221
...
...
@@ -60,15 +60,14 @@ object Seqstat extends ToolCommand {
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
Seqstat
=
{
val
seqstat
=
new
Seqstat
(
root
)
seqstat
.
input
=
input
seqstat
.
output
=
output
seqstat
.
output
=
new
File
(
output
,
input
.
getName
.
substring
(
0
,
input
.
getName
.
lastIndexOf
(
"."
))
+
".seqstats.json"
)
seqstat
}
def
apply
(
root
:
Configurable
,
fastqfile
:
File
,
outDir
:
String
)
:
Seqstat
=
{
val
seqstat
=
new
Seqstat
(
root
)
val
ext
=
fastqfile
.
getName
.
substring
(
fastqfile
.
getName
.
lastIndexOf
(
"."
))
seqstat
.
input
=
fastqfile
seqstat
.
output
=
new
File
(
outDir
+
fastqfile
.
getName
.
substring
(
0
,
fastqfile
.
getName
.
lastIndexOf
(
"."
))
+
".seqstats.json"
)
seqstat
.
output
=
new
File
(
outDir
,
fastqfile
.
getName
.
substring
(
0
,
fastqfile
.
getName
.
lastIndexOf
(
"."
))
+
".seqstats.json"
)
seqstat
}
...
...
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