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biopet.biopet
Commits
ce85fe0a
Commit
ce85fe0a
authored
Sep 22, 2015
by
Peter van 't Hof
Browse files
Added executable to command
parent
1dd927a3
Changes
1
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Inline
Side-by-side
public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
View file @
ce85fe0a
...
...
@@ -2,8 +2,9 @@ package nl.lumc.sasc.biopet.extensions.samtools
import
java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvanthof on 22/09/15.
...
...
@@ -19,12 +20,18 @@ class SamtoolsSort(val root: Configurable) extends Samtools {
var
compresion
:
Option
[
Int
]
=
config
(
"l"
)
var
outputFormat
:
Option
[
String
]
=
config
(
"O"
)
var
sortByName
:
Boolean
=
config
(
"sort_by_name"
,
default
=
false
)
va
l
prefix
:
String
=
config
(
"prefix"
,
default
=
new
File
(
qSettings
.
tempDirectory
,
output
.
getAbsolutePath
))
va
r
prefix
:
String
=
_
def
cmdLine
=
optional
(
"-m"
,
(
coreMemeory
+
"G"
))
+
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
prefix
=
config
(
"prefix"
,
default
=
new
File
(
Files
.
createTempDir
(),
output
.
getAbsolutePath
))
}
def
cmdLine
=
executable
+
required
(
"sort"
)
+
optional
(
"-m"
,
(
coreMemeory
+
"G"
))
+
optional
(
"-@"
,
threads
)
+
optional
(
"-O"
,
outputFormat
)
+
conditional
(
sortByName
,
"-n"
)
+
(
if
(
outputAsStsout
)
""
else
required
(
"-o"
,
output
))
+
(
if
(
outputAsStsout
)
""
else
required
(
"-o"
,
output
))
+
(
if
(
inputAsStdin
)
""
else
required
(
input
))
}
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