Commit 21452691 authored by Sander Bollen's avatar Sander Bollen
Browse files

use cached dict in reference

parent ab5dc438
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 {
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment