Commit c2087e09 authored by Sander Bollen's avatar Sander Bollen
Browse files

put bed conversion in kopisu method

parent b220a035
...@@ -42,6 +42,11 @@ ...@@ -42,6 +42,11 @@
<artifactId>BiopetExtensions</artifactId> <artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency> <dependency>
<groupId>org.testng</groupId> <groupId>org.testng</groupId>
<artifactId>testng</artifactId> <artifactId>testng</artifactId>
......
...@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.kopisu.methods ...@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.kopisu.methods
import nl.lumc.sasc.biopet.core.Reference import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.extensions.gatk.DepthOfCoverage import nl.lumc.sasc.biopet.extensions.gatk.DepthOfCoverage
import nl.lumc.sasc.biopet.extensions.tools.XcnvToBed
import nl.lumc.sasc.biopet.extensions.xhmm._ import nl.lumc.sasc.biopet.extensions.xhmm._
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
...@@ -98,6 +99,17 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { ...@@ -98,6 +99,17 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
genotype.outputVcf = new File(xhmmDir, "xhmm.vcf") genotype.outputVcf = new File(xhmmDir, "xhmm.vcf")
add(genotype) add(genotype)
// create bed files
val bedDir = new File(xhmmDir, "beds")
val beds = inputBams.keys.map{ x =>
val z = new XcnvToBed(this)
z.inputXcnv = discover.outputXcnv
z.sample = x
z.outpuBed = new File(bedDir, s"$x.bed")
z
}
addAll(beds)
addSummaryJobs() addSummaryJobs()
} }
......
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