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biopet.biopet
Commits
244ca457
Commit
244ca457
authored
Aug 11, 2014
by
Peter van 't Hof
Browse files
Added deps to constructor
parent
aa2484da
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala
View file @
244ca457
...
...
@@ -82,20 +82,22 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
}
object
Star
{
def
apply
(
configurable
:
Configurable
,
R1
:
File
,
R2
:
File
,
outputDir
:
String
,
isIntermediate
:
Boolean
=
false
)
:
Star
=
{
def
apply
(
configurable
:
Configurable
,
R1
:
File
,
R2
:
File
,
outputDir
:
String
,
isIntermediate
:
Boolean
=
false
,
deps
:
List
[
File
]
=
Nil
)
:
Star
=
{
val
star
=
new
Star
(
configurable
)
star
.
R1
=
R1
if
(
R2
!=
null
)
star
.
R2
=
R2
star
.
outputDir
=
outputDir
star
.
isIntermediate
=
isIntermediate
star
.
deps
=
deps
star
.
afterGraph
return
star
}
def
_2pass
(
configurable
:
Configurable
,
R1
:
File
,
R2
:
File
,
outputDir
:
String
,
isIntermediate
:
Boolean
=
false
)
:
(
File
,
List
[
Star
])
=
{
def
_2pass
(
configurable
:
Configurable
,
R1
:
File
,
R2
:
File
,
outputDir
:
String
,
isIntermediate
:
Boolean
=
false
,
deps
:
List
[
File
]
=
Nil
)
:
(
File
,
List
[
Star
])
=
{
val
outDir
=
if
(
outputDir
.
endsWith
(
"/"
))
outputDir
else
outputDir
+
"/"
val
starCommand_pass1
=
Star
(
configurable
,
R1
,
if
(
R2
!=
null
)
R2
else
null
,
outDir
+
"aln-pass1/"
)
starCommand_pass1
.
isIntermediate
=
isIntermediate
starCommand_pass1
.
deps
=
deps
starCommand_pass1
.
afterGraph
val
starCommand_reindex
=
new
Star
(
configurable
)
...
...
@@ -108,6 +110,7 @@ object Star {
val
starCommand_pass2
=
Star
(
configurable
,
R1
,
if
(
R2
!=
null
)
R2
else
null
,
outDir
+
"aln-pass2/"
)
starCommand_pass2
.
genomeDir
=
starCommand_reindex
.
outputDir
starCommand_pass2
.
isIntermediate
=
isIntermediate
starCommand_pass2
.
deps
=
deps
starCommand_pass2
.
afterGraph
return
(
starCommand_pass2
.
outputSam
,
List
(
starCommand_pass1
,
starCommand_reindex
,
starCommand_pass2
))
...
...
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