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biopet.biopet
Commits
d0768d9f
Commit
d0768d9f
authored
Aug 19, 2014
by
sajvanderzeeuw
Browse files
added all BWA options
parent
7ab284fd
Changes
1
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Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala
View file @
d0768d9f
...
...
@@ -68,6 +68,29 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
required
(
reference
)
+
required
(
R1
)
+
optional
(
R2
)
+
optional
(
"-w"
,
w
)
+
optional
(
"-d"
,
d
)
+
optional
(
"-c"
,
c
)
+
optional
(
"-D"
,
D
)
+
optional
(
"-W"
,
W
)
+
optional
(
"-m"
,
m
)
+
conditional
(
P
,
"-P"
)
+
conditional
(
e
,
"-e"
)
+
optional
(
"-A"
,
A
)
+
optional
(
"-B"
,
B
)
+
optional
(
"-O"
,
O
)
+
optional
(
"-E"
,
E
)
+
optional
(
"-L"
,
L
)
+
optional
(
"-U"
,
U
)
+
optional
(
"-x"
,
x
)
+
conditional
(
p
,
"-p"
)
+
optional
(
"-v"
,
v
)
+
optional
(
"-T"
,
T
)
+
optional
(
"-h"
,
h
)
+
conditional
(
a
,
"-a"
)
+
conditional
(
C
,
"-C"
)
+
conditional
(
Y
,
"-Y"
)
+
optional
(
"-I"
,
I
)
+
" > "
+
required
(
output
)
}
}
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