From 285e2e4d01c3eede401a0e034b3a8adef16bbd9d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 26 Feb 2015 14:11:25 +0100
Subject: [PATCH] Added implicit List[File]
---
.../extensions/gatk/broad/GatkGeneral.scala | 2 +-
.../lumc/sasc/biopet/utils/ConfigUtils.scala | 20 +++++++++++++++++++
2 files changed, 21 insertions(+), 1 deletion(-)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
index f390fa504..f3712fd54 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
@@ -21,5 +21,5 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
reference_sequence = config("reference")
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
- if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
+ if (config.contains("pedigree")) pedigree = config("pedigree")
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 2c9ae7e6a..eaea3ad41 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -313,6 +313,16 @@ object ConfigUtils extends Logging {
any2list(any).map(_.toString)
}
+ /**
+ * Convert Any to List[File]
+ * @param any Input Any value
+ * @return
+ */
+ def any2fileList(any: Any): List[File] = {
+ if (any == null) return null
+ any2list(any).map(x => new File(x.toString))
+ }
+
/**
* Convert Any to Map[String, Any]
* @param any Input Any value
@@ -505,6 +515,16 @@ object ConfigUtils extends Logging {
else Nil
}
+ /**
+ * Convert ConfigValue to List[File]
+ * @param value Input ConfigValue
+ * @return
+ */
+ implicit def configValue2fileList(value: ConfigValue): List[File] = {
+ if (requiredValue(value)) any2fileList(value.value)
+ else Nil
+ }
+
/**
* Convert ConfigValue to Set[String]
* @param value Input ConfigValue
--
GitLab