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biopet.biopet
Commits
e98f7409
Commit
e98f7409
authored
Mar 05, 2015
by
Peter van 't Hof
Browse files
Added scala docs for bedtools
parent
c58fbc6a
Changes
3
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
View file @
e98f7409
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/** General abstract class for bedtools extensions */
abstract
class
Bedtools
extends
BiopetCommandLineFunction
{
override
def
subPath
=
"bedtools"
::
super
.
subPath
executable
=
config
(
"exe"
,
default
=
"bedtools"
,
submodule
=
"bedtools"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
View file @
e98f7409
...
...
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
/** Extension for bedtools coverage */
class
BedtoolsCoverage
(
val
root
:
Configurable
)
extends
Bedtools
{
@Input
(
doc
=
"Input file (bed/gff/vcf/bam)"
)
var
input
:
File
=
_
...
...
@@ -44,6 +45,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
if
(
input
.
getName
.
endsWith
(
".bam"
))
inputTag
=
"-abam"
}
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"coverage"
)
+
required
(
inputTag
,
input
)
+
required
(
"-b"
,
intersectFile
)
+
...
...
@@ -54,6 +56,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
}
object
BedtoolsCoverage
{
/** Returns defaul bedtools coverage */
def
apply
(
root
:
Configurable
,
input
:
File
,
intersect
:
File
,
output
:
File
,
depth
:
Boolean
=
true
,
sameStrand
:
Boolean
=
false
,
diffStrand
:
Boolean
=
false
)
:
BedtoolsCoverage
=
{
val
bedtoolsCoverage
=
new
BedtoolsCoverage
(
root
)
...
...
@@ -63,6 +66,6 @@ object BedtoolsCoverage {
bedtoolsCoverage
.
depth
=
depth
bedtoolsCoverage
.
sameStrand
=
sameStrand
bedtoolsCoverage
.
diffStrand
=
diffStrand
return
bedtoolsCoverage
bedtoolsCoverage
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
View file @
e98f7409
...
...
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
/** Extension for bedtools intersect */
class
BedtoolsIntersect
(
val
root
:
Configurable
)
extends
Bedtools
{
@Input
(
doc
=
"Input file (bed/gff/vcf/bam)"
)
var
input
:
File
=
_
...
...
@@ -41,6 +42,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
if
(
input
.
getName
.
endsWith
(
".bam"
))
inputTag
=
"-abam"
}
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"intersect"
)
+
required
(
inputTag
,
input
)
+
required
(
"-b"
,
intersectFile
)
+
...
...
@@ -50,6 +52,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
}
object
BedtoolsIntersect
{
/** Returns default bedtools intersect */
def
apply
(
root
:
Configurable
,
input
:
File
,
intersect
:
File
,
output
:
File
,
minOverlap
:
Double
=
0
,
count
:
Boolean
=
false
)
:
BedtoolsIntersect
=
{
val
bedtoolsIntersect
=
new
BedtoolsIntersect
(
root
)
...
...
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