From de250d3f037232a11bfd8bd186987bcc6ffc3084 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 15 Jan 2016 15:01:14 +0100
Subject: [PATCH] Fix pindel caller (fixing null error with Option[File] = None
instead of _)
---
.../lumc/sasc/biopet/extensions/pindel/PindelCaller.scala | 6 +++---
.../lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index a3204c20f..b807145a6 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -20,7 +20,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
/**
* Extension for pindel
@@ -47,10 +47,10 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
var input: File = _
@Argument(doc = "The pindel configuration file")
- var pindel_file: Option[File] = _
+ var pindel_file: Option[File] = None
@Argument(doc = "Configuration file with: bam-location/insert size/name")
- var config_file: Option[File] = _
+ var config_file: Option[File] = None
@Argument(doc = "Work directory")
var output_prefix: File = _
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
index 0bccf63d8..0e0aed54f 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -32,7 +32,7 @@ class Pindel(val root: Configurable) extends SvCaller {
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(outputDir + "." + sample + ".pindel.cfg")
val cfg = new PindelConfig(this)
cfg.input = bamFile
--
GitLab