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biopet.biopet
Commits
e42f7355
Commit
e42f7355
authored
Jan 14, 2016
by
Wai Yi Leung
Browse files
Fix compile errors
parent
d1384de8
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
View file @
e42f7355
...
...
@@ -166,7 +166,7 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
optional
(
"--MIN_DD_CLUSTER_SIZE"
,
MIN_DD_CLUSTER_SIZE
)
+
optional
(
"--MIN_DD_BREAKPOINT_SUPPORT"
,
MIN_DD_BREAKPOINT_SUPPORT
)
+
optional
(
"--MIN_DD_MAP_DISTANCE"
,
MIN_DD_MAP_DISTANCE
)
+
optional
(
"--DD_REPORT_DUPLICATION_READS"
,
DD_REPORT_DUPLICATION_READS
)
+
optional
(
"--DD_REPORT_DUPLICATION_READS"
,
DD_REPORT_DUPLICATION_READS
)
}
object
PindelCaller
{
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
View file @
e42f7355
...
...
@@ -14,8 +14,8 @@
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.pindel
import
java.io.
{
PrintWriter
,
File
}
import
collection.JavaConversions._
import
java.io.
{
PrintWriter
,
File
}
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
...
...
@@ -70,16 +70,13 @@ object PindelConfig extends ToolCommand {
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
val
input
:
File
=
commandArgs
.
inputbam
val
output
:
File
=
commandArgs
.
output
.
getOrElse
(
new
File
(
input
.
getAbsoluteFile
+
".pindel.cfg"
)
)
val
output
:
File
=
commandArgs
.
output
.
getOrElse
(
new
File
(
input
.
getAbsoluteFile
+
".pindel.cfg"
))
val
insertsize
:
Int
=
commandArgs
.
insertsize
.
getOrElse
(
0
)
val
bamReader
=
SamReaderFactory
.
makeDefault
().
open
(
input
)
val
writer
=
new
PrintWriter
(
output
)
var
sampleName
:
String
=
""
for
(
readgroup
<-
bamReader
.
getFileHeader
.
getReadGroups
()
)
{
val
rg
=
bamReader
.
getFileHeader
.
getReadGroup
(
readgroup
)
writer
.
write
(
s
"${input.getAbsoluteFile}\t${insertsize}\t${rg.getSample}"
)
for
(
readgroup
<-
bamReader
.
getFileHeader
.
getReadGroups
().
toList
)
{
writer
.
write
(
s
"${input.getAbsoluteFile}\t${insertsize}\t${readgroup.getSample}\n"
)
}
bamReader
.
close
()
writer
.
close
()
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
View file @
e42f7355
...
...
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.pindel.
{
PindelCaller
,
PindelCaller
$
,
PindelConfig
}
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.pindel.
{
PindelCaller
,
PindelCaller
$
,
PindelConfig
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -27,35 +27,12 @@ class Pindel(val root: Configurable) extends SvCaller {
val
name
=
"pindel"
def
this
()
=
this
(
null
)
//
// @Input(doc = "Input file (bam)")
// var input: File = _
//
// @Input(doc = "Reference Fasta file")
// var reference: File = _
//
// @Argument(doc = "Work directory")
// var workdir: String = _
//
// // @Output(doc = "Pindel VCF output")
// // lazy val outputvcf: File = {
// // new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
// // }
//
// @Output(doc = "Pindel config")
// def configfile: File = {
// new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.cfg")
// }
// @Output(doc = "Pindel raw output")
// def outputvcf: File = {
// new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
// }
def
biopetScript
()
{
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
pindelDir
=
new
File
(
outputDir
,
sample
)
val
config_file
:
File
=
new
File
(
bamFile
.
getAbsolutePath
+
".pindel.cfg"
)
val
config_file
:
File
=
new
File
(
bamFile
.
getAbsolutePath
+
".pindel.cfg"
)
val
cfg
=
new
PindelConfig
(
this
)
cfg
.
input
=
bamFile
...
...
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