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biopet.biopet
Commits
21452691
Commit
21452691
authored
Oct 26, 2016
by
Sander Bollen
Browse files
use cached dict in reference
parent
ab5dc438
Changes
1
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kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala
View file @
21452691
package
nl.lumc.sasc.biopet.pipelines.kopisu.methods
import
htsjdk.samtools.
{
SAMSequenceDictionary
,
SamReaderFactory
}
import
htsjdk.samtools.
{
SAMSequenceDictionary
,
SamReaderFactory
}
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.extensions.Cnmops
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -9,18 +10,13 @@ import scala.collection.JavaConversions._
/**
* Created by wyleung on 2-6-16.
*/
class
CnmopsMethod
(
val
root
:
Configurable
)
extends
CnvMethod
{
class
CnmopsMethod
(
val
root
:
Configurable
)
extends
CnvMethod
with
Reference
{
def
name
=
"cnmops"
def
biopetScript
:
Unit
=
{
val
genomeContigs
:
SAMSequenceDictionary
=
SamReaderFactory
.
makeDefault
.
referenceSequence
(
referenceFasta
)
.
getFileHeader
(
referenceDict
)
.
getSequenceDictionary
// we repeat running cnmops for all chromosomes
val
cnmopsJobs
=
genomeContigs
.
getSequences
.
map
(
contig
=>
{
val
cnmopsJobs
=
referenceDict
.
getSequences
.
map
(
contig
=>
{
val
cnmops
=
new
Cnmops
(
this
)
cnmops
.
chromosome
=
contig
.
getSequenceName
cnmops
.
input
=
inputBams
.
flatMap
{
...
...
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