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biopet.biopet
Commits
9c66f418
Commit
9c66f418
authored
Apr 16, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 16, 2017
Browse files
Merge branch 'develop' into fix-BIOPET-368
parents
077a520a
1f2295c2
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
9c66f418
...
...
@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var
R2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"R"
)
var
reference
:
File
=
null
var
reference
:
File
=
_
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
...
...
@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var
k
:
Option
[
Int
]
=
config
(
"k"
)
var
r
:
Option
[
Float
]
=
config
(
"r"
)
var
S
:
Boolean
=
config
(
"S"
,
default
=
false
)
var
M
:
Boolean
=
config
(
"M"
,
default
=
tru
e
)
var
M
:
Boolean
=
config
(
"M"
,
default
=
fals
e
)
var
w
:
Option
[
Int
]
=
config
(
"w"
)
var
d
:
Option
[
Int
]
=
config
(
"d"
)
var
c
:
Option
[
Int
]
=
config
(
"c"
)
...
...
@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
def
cmdLine
=
{
def
cmdLine
:
String
=
{
required
(
executable
)
+
required
(
"mem"
)
+
optional
(
"-k"
,
k
)
+
...
...
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