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biopet.biopet
Commits
4ddf34bf
Commit
4ddf34bf
authored
Aug 18, 2014
by
sajvanderzeeuw
Browse files
Added all BWA mem options
parent
c36fb267
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala
View file @
4ddf34bf
...
...
@@ -18,10 +18,36 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
var
RG
:
String
=
_
var
R
:
String
=
config
(
"R"
)
var
k
:
Option
[
Int
]
=
config
(
"k"
)
var
r
:
Option
[
Float
]
=
config
(
"r"
)
var
S
:
Boolean
=
config
(
"S"
)
var
M
:
Boolean
=
config
(
"M"
,
default
=
true
)
var
w
:
Option
[
Int
]
=
config
(
"w"
)
var
d
:
Option
[
Int
]
=
config
(
"d"
)
var
c
:
Option
[
Int
]
=
config
(
"c"
)
var
D
:
Option
[
Float
]
=
config
(
"D"
)
var
W
:
Option
[
Int
]
=
config
(
"W"
)
var
m
:
Option
[
Int
]
=
config
(
"m"
)
var
P
:
Boolean
=
config
(
"P"
)
var
e
:
Boolean
=
config
(
"e"
)
var
A
:
Option
[
Int
]
=
config
(
"A"
)
var
B
:
Option
[
Int
]
=
config
(
"B"
)
var
O
:
String
=
config
(
"O"
)
var
E
:
String
=
config
(
"E"
)
var
L
:
String
=
config
(
"L"
)
var
U
:
Option
[
Int
]
=
config
(
"U"
)
var
x
:
String
=
config
(
"x"
)
var
p
:
Boolean
=
config
(
"p"
)
var
v
:
Option
[
Int
]
=
config
(
"v"
)
var
T
:
Option
[
Int
]
=
config
(
"T"
)
var
h
:
Option
[
Int
]
=
config
(
"h"
)
var
a
:
Boolean
=
config
(
"a"
)
var
C
:
Boolean
=
config
(
"C"
)
var
Y
:
Boolean
=
config
(
"Y"
)
var
I
:
String
=
config
(
"I"
)
executable
=
config
(
"exe"
,
default
=
"bwa"
)
executable
=
config
(
"exe"
,
default
=
"bwa"
,
freeVar
=
false
)
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
...
...
@@ -33,9 +59,12 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
def
cmdLine
=
{
required
(
executable
)
+
required
(
"mem"
)
+
optional
(
"-k"
,
k
)
+
optional
(
"-r"
,
r
)
+
optional
(
"-t"
,
nCoresRequest
)
+
optional
(
"-R"
,
R
G
)
+
optional
(
"-R"
,
R
)
+
conditional
(
M
,
"-M"
)
+
conditional
(
S
,
"-S"
)
+
required
(
reference
)
+
required
(
R1
)
+
optional
(
R2
)
+
...
...
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