Merge pull request #5 from biopet/fix-BIOPET-519

Fix BIOPET-519

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala

@@ -18,9 +18,9 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
 import nl.lumc.sasc.biopet.core.extensions.Md5sum
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
-import org.broadinstitute.gatk.queue.{QScript, QSettings}
+import org.broadinstitute.gatk.queue.{ QScript, QSettings }
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala

 package nl.lumc.sasc.biopet.core
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import com.google.common.io.Files
 import org.scalatest.Matchers
@@ -11,8 +11,8 @@ import nl.lumc.sasc.biopet.utils.IoUtils._
 import org.apache.commons.io.FileUtils
 
 /**
-  * Created by pjvan_thof on 10-1-17.
-  */
+ * Created by pjvan_thof on 10-1-17.
+ */
 class PipelineStatusTest extends TestNGSuite with Matchers {
   @Test
   def testDefault(): Unit = {

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala

@@ -14,7 +14,7 @@
  */
 package nl.lumc.sasc.biopet.tools.vcfstats
 
-import java.io.{ File, FileOutputStream, PrintWriter }
+import java.io.{ File, FileOutputStream, IOException, PrintWriter }
 
 import htsjdk.samtools.util.Interval
 import htsjdk.variant.variantcontext.{ Genotype, VariantContext }
@@ -557,11 +557,17 @@ object VcfStats extends ToolCommand {
     val command: String = "Rscript " + file + " " + args.mkString(" ")
 
     logger.info("Starting: " + command)
-    val process = Process(command).run(ProcessLogger(x => logger.debug(x), x => logger.debug(x)))
-    if (process.exitValue() == 0) logger.info("Done: " + command)
-    else {
-      logger.warn("Failed: " + command)
-      if (!logger.isDebugEnabled) logger.warn("Use -l debug for more info")
+    try {
+      val process = Process(command).run(ProcessLogger(x => logger.debug(x), x => logger.debug(x)))
+      if (process.exitValue() == 0) logger.info("Done: " + command)
+      else {
+        logger.warn("Failed: " + command)
+        if (!logger.isDebugEnabled) logger.warn("Use -l debug for more info")
+      }
+    } catch {
+      case e: IOException =>
+        logger.warn("Failed: " + command)
+        logger.debug(e)
     }
   }
 }

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala

@@ -103,7 +103,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testMergeStatsMap = {
+  def testMergeStatsMap() = {
     val m1: mutable.Map[Any, Int] = mutable.Map("a" -> 1)
     val m2: mutable.Map[Any, Int] = mutable.Map("b" -> 2)
 
@@ -124,7 +124,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testMergeNestedStatsMap = {
+  def testMergeNestedStatsMap() = {
     val m1: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map("test" ->
       mutable.Map("nested" -> mutable.Map("a" -> 1)))
     val m2: Map[String, Map[String, Map[Any, Int]]] = Map("test" ->
@@ -152,7 +152,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testValueOfTsv = {
+  def testValueOfTsv() = {
     val i = new File(resourcePath("/sample.tsv"))
 
     valueFromTsv(i, "Sample_ID_1", "library") should be(Some("Lib_ID_1"))
@@ -163,7 +163,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testMain = {
+  def testMain() = {
     val tmp = Files.createTempDirectory("vcfStats")
     val vcf = resourcePath("/chrQ.vcf.gz")
     val ref = resourcePath("/fake_chrQ.fa")
@@ -229,7 +229,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testSortAnyAny = {
+  def testSortAnyAny() = {
     //stub
     val one: Any = 1
     val two: Any = 2
@@ -245,7 +245,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testCheckGeneral = {
+  def testCheckGeneral() = {
     val record = new VCFFileReader(new File(resourcePath("/chrQ.vcf.gz"))).iterator().next()
 
     val blah = checkGeneral(record, List())
@@ -253,7 +253,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     blah.get("chrQ") should not be empty
     blah.get("total") should not be empty
 
-    val chrq = blah.get("chrQ").get
+    val chrq = blah("chrQ")
     chrq.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
     chrq.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
     chrq.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
@@ -269,7 +269,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     chrq.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
 
     chrq.get("general") should not be empty
-    val general = chrq.get("general").get
+    val general = chrq("general")
 
     general.get("PolymorphicInSamples") shouldEqual Some(1)
     general.get("ComplexIndel") shouldEqual Some(0)
@@ -291,7 +291,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     general.get("Symbolic") shouldEqual Some(0)
     general.get("SimpleInsertion") shouldEqual Some(1)
 
-    val total = blah.get("total").get
+    val total = blah("total")
     total.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
     total.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
     total.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
@@ -307,7 +307,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     total.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
 
     chrq.get("general") should not be empty
-    val totGeneral = total.get("general").get
+    val totGeneral = total("general")
 
     totGeneral.get("PolymorphicInSamples") shouldEqual Some(1)
     totGeneral.get("ComplexIndel") shouldEqual Some(0)
@@ -331,7 +331,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testCheckGenotype = {
+  def testCheckGenotype() = {
     val record = new VCFFileReader(new File(resourcePath("/chrQ.vcf.gz"))).iterator().next()
 
     val genotype = record.getGenotype(0)
@@ -341,7 +341,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     blah.get("chrQ") should not be empty
     blah.get("total") should not be empty
 
-    val chrq = blah.get("chrQ").get
+    val chrq = blah("chrQ")
     chrq.get("GQ") shouldEqual Some(Map(99 -> 1))
     chrq.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
     chrq.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
@@ -350,7 +350,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     chrq.get("AD-ref") shouldEqual Some(Map(24 -> 1))
     chrq.get("general") should not be empty
 
-    val general = chrq.get("general").get
+    val general = chrq("general")
     general.get("Hom") shouldEqual Some(0)
     general.get("NoCall") shouldEqual Some(0)
     general.get("Variant") shouldEqual Some(1)
@@ -365,7 +365,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     general.get("Het") shouldEqual Some(1)
     general.get("HetNonRef") shouldEqual Some(0)
 
-    val total = blah.get("total").get
+    val total = blah("total")
     total.get("GQ") shouldEqual Some(Map(99 -> 1))
     total.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
     total.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
@@ -374,7 +374,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
     total.get("AD-ref") shouldEqual Some(Map(24 -> 1))
     total.get("general") should not be empty
 
-    val totGeneral = total.get("general").get
+    val totGeneral = total("general")
     totGeneral.get("Hom") shouldEqual Some(0)
     totGeneral.get("NoCall") shouldEqual Some(0)
     totGeneral.get("Variant") shouldEqual Some(1)

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala

@@ -14,9 +14,10 @@
  */
 package nl.lumc.sasc.biopet.utils
 
-import java.io.{ File, FileInputStream, FileOutputStream, InputStream }
+import java.io._
 
 import scala.io.Source
+import scala.sys.process.Process
 
 /**
  * This object contains generic io methods
@@ -83,4 +84,13 @@ object IoUtils {
     reader.close()
     lines
   }
+
+  def executableExist(exe: String): Boolean = {
+    try {
+      val process = Process(Seq(exe)).run()
+      true
+    } catch {
+      case e: IOException => false
+    }
+  }
 }

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -204,6 +204,7 @@ object ShivaTest {
     "fastqc" -> Map("exe" -> "test"),
     "input_alleles" -> "test",
     "variantcallers" -> "raw",
+    "rscript" -> Map("exe" -> "test"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
     "sickle" -> Map("exe" -> "test"),

tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala

@@ -129,6 +129,7 @@ object TinyCapTest {
     "annotation_refflat" -> annotationRefflat,
 
     "md5sum" -> Map("exe" -> "test"),
+    "rscript" -> Map("exe" -> "test"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
     "sickle" -> Map("exe" -> "test"),