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biopet.biopet
Commits
ca7bf0d9
Commit
ca7bf0d9
authored
Apr 12, 2017
by
Peter van 't Hof
Browse files
Adding missing options
parent
7a95865b
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
View file @
ca7bf0d9
...
...
@@ -21,7 +21,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sambemba markdup */
class
SambambaMarkdup
(
val
parent
:
Configurable
)
extends
Sambamba
{
override
def
defaultThreads
=
4
@Input
(
doc
=
"Bam File"
)
var
input
:
File
=
_
...
...
@@ -32,10 +31,14 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
var
removeDuplicates
:
Boolean
=
config
(
"remove_duplicates"
,
default
=
false
)
// @doc: compression_level 6 is average, 0 = no compression, 9 = best
val
compressionLevel
:
Option
[
Int
]
=
config
(
"compression_level"
,
default
=
6
)
val
hashTableSize
:
Option
[
Int
]
=
config
(
"hash-table-size"
,
default
=
262144
)
val
overflowListSize
:
Option
[
Int
]
=
config
(
"overflow-list-size"
,
default
=
200000
)
val
ioBufferSize
:
Option
[
Int
]
=
config
(
"io-buffer-size"
,
default
=
128
)
val
compressionLevel
:
Option
[
Int
]
=
config
(
"compression_level"
)
val
hashTableSize
:
Option
[
Int
]
=
config
(
"hash-table-size"
)
val
overflowListSize
:
Option
[
Int
]
=
config
(
"overflow-list-size"
)
val
ioBufferSize
:
Option
[
Int
]
=
config
(
"io-buffer-size"
)
val
showProgress
:
Boolean
=
config
(
"show-progress"
,
default
=
true
)
override
def
defaultThreads
=
4
override
def
defaultCoreMemory
=
4.0
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
...
...
@@ -43,6 +46,7 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
conditional
(
removeDuplicates
,
"--remove-duplicates"
)
+
optional
(
"-t"
,
nCoresRequest
)
+
optional
(
"-l"
,
compressionLevel
)
+
conditional
(
showProgress
,
"--show-progress"
)
+
optional
(
"--hash-table-size="
,
hashTableSize
,
spaceSeparated
=
false
)
+
optional
(
"--overflow-list-size="
,
overflowListSize
,
spaceSeparated
=
false
)
+
optional
(
"--io-buffer-size="
,
ioBufferSize
,
spaceSeparated
=
false
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
View file @
ca7bf0d9
...
...
@@ -30,13 +30,22 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
var
output
:
File
=
_
// @doc: compression_level 6 is average, 0 = no compression, 9 = best
val
compressionLevel
:
Option
[
Int
]
=
config
(
"compression_level"
,
default
=
6
)
val
compressionLevel
:
Option
[
Int
]
=
config
(
"compression_level"
)
val
header
:
Boolean
=
config
(
"header"
,
default
=
false
)
val
showProgress
:
Boolean
=
config
(
"show-progress"
,
default
=
true
)
val
filter
:
Option
[
String
]
=
config
(
"filter"
)
override
def
defaultThreads
=
4
override
def
defaultCoreMemory
=
4.0
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"merge"
)
+
optional
(
"-t"
,
nCoresRequest
)
+
optional
(
"-l"
,
compressionLevel
)
+
optional
(
"-F"
,
filter
)
+
conditional
(
header
,
"--header"
)
+
conditional
(
showProgress
,
"--show-progress"
)
+
required
(
output
)
+
repeat
(
""
,
input
)
}
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