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biopet.biopet
Commits
ff81ebd3
Commit
ff81ebd3
authored
Jan 16, 2015
by
Peter van 't Hof
Browse files
Added sampe
parent
1f867d68
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
0 → 100644
View file @
ff81ebd3
package
nl.lumc.sasc.biopet.extensions.bwa
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvan_thof on 1/16/15.
*/
class
BwaSampe
(
val
root
:
Configurable
)
extends
Bwa
{
@Input
(
doc
=
"Fastq file R1"
,
required
=
true
)
var
fastqR1
:
File
=
_
@Input
(
doc
=
"Fastq file R2"
,
required
=
true
)
var
fastqR2
:
File
=
_
@Input
(
doc
=
"Sai file R1"
,
required
=
true
)
var
saiR1
:
File
=
_
@Input
(
doc
=
"Sai file R2"
,
required
=
true
)
var
saiR2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
@Output
(
doc
=
"Output file SAM"
,
required
=
false
)
var
output
:
File
=
_
var
a
:
Option
[
Int
]
=
config
(
"a"
)
var
o
:
Option
[
Int
]
=
config
(
"o"
)
var
n
:
Option
[
Int
]
=
config
(
"n"
)
var
N
:
Option
[
Int
]
=
config
(
"N"
)
var
c
:
Option
[
Float
]
=
config
(
"c"
)
var
P
:
Boolean
=
config
(
"P"
,
default
=
false
)
var
s
:
Boolean
=
config
(
"s"
,
default
=
false
)
var
A
:
Boolean
=
config
(
"A"
,
default
=
false
)
var
r
:
String
=
_
def
cmdLine
=
required
(
executable
)
+
required
(
"samse"
)
+
optional
(
"-n"
,
n
)
+
optional
(
"-f"
,
output
)
+
optional
(
"-r"
,
r
)
+
optional
(
"-c"
,
c
)
+
conditional
(
P
,
"-P"
)
+
conditional
(
s
,
"-s"
)
+
conditional
(
A
,
"-A"
)
+
required
(
reference
)
+
required
(
saiR1
)
+
required
(
saiR2
)
+
required
(
fastqR1
)
+
required
(
fastqR2
)
}
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