Merge branch 'hotfix-0.1.4' into 'master'

Hotfix 0.1.4

Fix breaking bug on vcffilter tool

See merge request !14

biopet-framework/pom.xml

@@ -4,7 +4,7 @@
 
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>BiopetFramework</artifactId>
-  <version>0.1.3</version>
+  <version>0.1.4</version>
   <packaging>jar</packaging>
 
   <name>BiopetFramework</name>

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

@@ -111,7 +111,7 @@ object VcfFilter extends ToolCommand {
           
       if (record.getAttributeAsInt("DP", -1) >= commandArgs.minTotalDepth && 
           genotypes.count(_ == true) >= commandArgs.minSamplesPass &&
-          bamADvalues.count(_ == true) >= commandArgs.minSamplesPass)
+          (commandArgs.minBamAlternateDepth <= 0 || bamADvalues.count(_ == true) >= commandArgs.minSamplesPass))
         writer.add(record)
     }
     reader.close