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biopet.biopet
Commits
5571a0d7
Commit
5571a0d7
authored
Sep 01, 2014
by
Peter van 't Hof
Browse files
Added more options for bowtie
parent
2df385bf
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bowtie.scala
View file @
5571a0d7
...
...
@@ -27,13 +27,27 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
override
val
defaultThreads
=
8
var
sam
:
Boolean
=
config
(
"sam"
,
default
=
true
)
var
sam_RG
:
String
=
_
var
sam_RG
:
String
=
config
(
"sam-RG"
)
var
seedlen
:
Option
[
Int
]
=
config
(
"seedlen"
)
var
k
:
Option
[
Int
]
=
config
(
"k"
)
var
m
:
Option
[
Int
]
=
config
(
"m"
)
var
best
:
Boolean
=
config
(
"best"
)
var
maxbts
:
Option
[
Int
]
=
config
(
"maxbts"
)
var
strata
:
Boolean
=
config
(
"strata"
)
var
maqerr
:
Option
[
Int
]
=
config
(
"maqerr"
)
def
cmdLine
=
{
required
(
executable
)
+
optional
(
"--threads"
,
nCoresRequest
)
+
conditional
(
sam
,
"--sam"
)
+
required
(
"--sam-RG"
,
sam_RG
)
+
conditional
(
best
,
"--best"
)
+
conditional
(
strata
,
"--strata"
)
+
optional
(
"--sam-RG"
,
sam_RG
)
+
optional
(
"--seedlen"
,
seedlen
)
+
optional
(
"--k"
,
k
)
+
optional
(
"--m"
,
m
)
+
optional
(
"--maxbts"
,
maxbts
)
+
optional
(
"--maqerr"
,
maqerr
)
+
required
(
reference
)
+
required
(
R1
)
+
optional
(
R2
)
+
...
...
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