From e5d886e42779dab4fe200c09e0643e241f3e52b4 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 25 Jun 2015 16:31:55 +0200
Subject: [PATCH] Wrap Picard dependency list fetch in Option
---
.../biopet/extensions/picard/Picard.scala | 40 ++++++++++---------
1 file changed, 22 insertions(+), 18 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index d4f60ee54..be22486e7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -82,25 +82,29 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
object Picard extends Logging {
lazy val getBiopetPicardVersion: Option[String] = {
- val reader = Source.fromInputStream(getClass.getResourceAsStream("/dependency_list.txt"))
- val dependencies = reader.getLines().map(_.trim.split(":")).filter(_.size == 5).map(line => Map(
- "groupId" -> line(0),
- "artifactId" -> line(1),
- "type" -> line(2),
- "version" -> line(3),
- "scope" -> line(4)
- )).toList
-
- logger.debug("dependencies: " + dependencies)
-
- val htsjdk = dependencies.find(dep => dep("groupId") == "samtools" && dep("artifactId") == "htsjdk").collect {
- case dep =>
- "samtools htsjdk " + dep("version")
- }
+ Option(getClass.getResourceAsStream("/dependency_list.txt")) match {
+ case Some(src) =>
+ val dependencies = Source.fromInputStream(src)
+ .getLines().map(_.trim.split(":")).filter(_.size == 5).map(line => Map(
+ "groupId" -> line(0),
+ "artifactId" -> line(1),
+ "type" -> line(2),
+ "version" -> line(3),
+ "scope" -> line(4)
+ )).toList
+
+ logger.debug("dependencies: " + dependencies)
+
+ val htsjdk = dependencies.find(dep => dep("groupId") == "samtools" && dep("artifactId") == "htsjdk").collect {
+ case dep =>
+ "samtools htsjdk " + dep("version")
+ }
- dependencies.find(dep => dep("groupId") == "picard" && dep("artifactId") == "picard").collect {
- case dep =>
- "Picard " + dep("version") + " using " + htsjdk.getOrElse("unknown htsjdk")
+ dependencies.find(dep => dep("groupId") == "picard" && dep("artifactId") == "picard").collect {
+ case dep =>
+ "Picard " + dep("version") + " using " + htsjdk.getOrElse("unknown htsjdk")
+ }
+ case otherwise => None
}
}
--
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