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biopet.biopet
Commits
217f72ff
Commit
217f72ff
authored
Sep 01, 2014
by
Peter van 't Hof
Browse files
Added seedmms option
parent
6d77359f
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 @
217f72ff
...
...
@@ -29,6 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var
sam
:
Boolean
=
config
(
"sam"
,
default
=
true
)
var
sam_RG
:
String
=
config
(
"sam-RG"
)
var
seedlen
:
Option
[
Int
]
=
config
(
"seedlen"
)
var
seedmms
:
Option
[
Int
]
=
config
(
"seedmms"
)
var
k
:
Option
[
Int
]
=
config
(
"k"
)
var
m
:
Option
[
Int
]
=
config
(
"m"
)
var
best
:
Boolean
=
config
(
"best"
)
...
...
@@ -44,8 +45,9 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
conditional
(
strata
,
"--strata"
)
+
optional
(
"--sam-RG"
,
sam_RG
)
+
optional
(
"--seedlen"
,
seedlen
)
+
optional
(
"--k"
,
k
)
+
optional
(
"--m"
,
m
)
+
optional
(
"--seedmms"
,
seedmms
)
+
optional
(
"-k"
,
k
)
+
optional
(
"-m"
,
m
)
+
optional
(
"--maxbts"
,
maxbts
)
+
optional
(
"--maqerr"
,
maqerr
)
+
required
(
reference
)
+
...
...
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