From 14fa14d5d403f94cacb5bb9d5cd44769c31aa7a1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 25 Sep 2015 13:03:49 +0200
Subject: [PATCH] Added aggregate option for scoverage
---
pom.xml | 2 +-
.../scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 2 +-
public/pom.xml | 9 +++------
3 files changed, 5 insertions(+), 8 deletions(-)
diff --git a/pom.xml b/pom.xml
index 506f96b6d..964da3f4a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -17,6 +17,6 @@
<module>public</module>
<module>protected</module>
<module>external-example</module>
- <module>biopet-aggregate</module>
+ <!--<module>biopet-aggregate</module>-->
</modules>
</project>
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index fa714c942..f3c1a41a6 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -94,7 +94,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
}
-
+
this match {
case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
logger.info("Write report is skipped because sample flag is used")
diff --git a/public/pom.xml b/public/pom.xml
index 3c49b66c1..3cb8ecd06 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -51,6 +51,7 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<scoverage.plugin.version>1.1.1</scoverage.plugin.version>
+ <scalaVersion>2.10.4</scalaVersion>
</properties>
<build>
@@ -243,14 +244,10 @@
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
<configuration>
- <scalaVersion>2.10.2</scalaVersion>
+ <scalaVersion>${scalaVersion}</scalaVersion>
+ <aggregate>true</aggregate>
<!-- other parameters -->
</configuration>
- <executions>
- <execution>
- <phase>test</phase>
- </execution>
- </executions>
</plugin>
</plugins>
</build>
--
GitLab