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biopet.biopet
Commits
6b69a6d5
Commit
6b69a6d5
authored
Aug 25, 2014
by
Peter van 't Hof
Browse files
Added -s and -S option
parent
1f6b6d87
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
View file @
6b69a6d5
...
...
@@ -16,6 +16,12 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
@Argument
(
doc
=
"dept"
,
required
=
false
)
var
depth
:
Boolean
=
false
@Argument
(
doc
=
"sameStrand"
,
required
=
false
)
var
sameStrand
:
Boolean
=
false
@Argument
(
doc
=
"diffStrand"
,
required
=
false
)
var
diffStrand
:
Boolean
=
false
var
inputTag
=
"-a"
...
...
@@ -27,17 +33,21 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
required
(
inputTag
,
input
)
+
required
(
"-b"
,
intersectFile
)
+
conditional
(
depth
,
"-d"
)
+
conditional
(
sameStrand
,
"-s"
)
+
conditional
(
diffStrand
,
"-S"
)
+
" > "
+
required
(
output
)
}
object
BedtoolsCoverage
{
def
apply
(
root
:
Configurable
,
input
:
File
,
intersect
:
File
,
output
:
File
,
depth
:
Boolean
=
true
)
:
BedtoolsCoverage
=
{
depth
:
Boolean
=
true
,
sameStrand
:
Boolean
=
false
,
diffStrand
:
Boolean
=
false
)
:
BedtoolsCoverage
=
{
val
bedtoolsCoverage
=
new
BedtoolsCoverage
(
root
)
bedtoolsCoverage
.
input
=
input
bedtoolsCoverage
.
intersectFile
=
intersect
bedtoolsCoverage
.
output
=
output
bedtoolsCoverage
.
depth
=
depth
bedtoolsCoverage
.
sameStrand
=
sameStrand
bedtoolsCoverage
.
diffStrand
=
diffStrand
return
bedtoolsCoverage
}
}
\ No newline at end of file
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