From 9db6c09d8ff1aa3ed0d9a2736381a31a749b414c Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 15 Jan 2016 15:09:41 +0100
Subject: [PATCH] Fix major error, things in beforeCmd was intended to do in
beforeGraph
---
.../sasc/biopet/extensions/pindel/PindelCaller.scala | 10 +++++-----
1 file changed, 5 insertions(+), 5 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 b807145a6..c83f12e17 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
@@ -104,19 +104,19 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
var MIN_DD_MAP_DISTANCE: Option[Int] = config("MIN_DD_MAP_DISTANCE")
var DD_REPORT_DUPLICATION_READS: Option[Int] = config("DD_REPORT_DUPLICATION_READS")
- override def beforeCmd(): Unit = {
+ override def beforeGraph: Unit = {
// we should check whether the `pindel-config-file` is set or the `config-file` for the bam-list
// at least one of them should be set.
(pindel_file, config_file) match {
case (None, None) => Logging.addError("No pindel config is given")
case (Some(a), Some(b)) => Logging.addError(s"Please specify either a pindel config or bam-config. Not both for Pindel: $a or $b")
case (Some(a), None) => {
- Logging.logger.info(s"Using $pindel_file as pindel config for Pindel")
- input = a
+ Logging.logger.info(s"Using '${a}' as pindel config for Pindel")
+ input = a.getAbsoluteFile
}
case (None, Some(b)) => {
- Logging.logger.info(s"Using $config_file as bam config for Pindel")
- input = b
+ Logging.logger.info(s"Using '${b}' as bam config for Pindel")
+ input = b.getAbsoluteFile
}
}
}
--
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