Commit 08bcca4d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Each aligner has his own class now

parent ba0cf48a
......@@ -36,7 +36,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
*
* Created by pjvan_thof on 2/12/15.
*/
class MappingTest extends TestNGSuite with Matchers {
abstract class AbstractTestMapping extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Mapping = {
new Mapping {
override def configName = "mapping"
......@@ -46,6 +46,8 @@ class MappingTest extends TestNGSuite with Matchers {
}
}
val aligner: String
@DataProvider(name = "mappingOptions")
def mappingOptions = {
val aligners = Array("bwa-mem", "bwa-aln", "star", "star-2pass", "bowtie", "stampy", "gsnap", "tophat")
......@@ -56,7 +58,6 @@ class MappingTest extends TestNGSuite with Matchers {
val zipped = Array(true, false)
for (
aligner <- aligners;
pair <- paired;
chunk <- chunks;
skipMarkDuplicate <- skipMarkDuplicates;
......@@ -99,7 +100,42 @@ class MappingTest extends TestNGSuite with Matchers {
}
}
class MappingBwaMemTest extends AbstractTestMapping {
val aligner = "bwa-mem"
}
class MappingBwaAlnTest extends AbstractTestMapping {
val aligner = "bwa-aln"
}
class MappingStarTest extends AbstractTestMapping {
val aligner = "star"
}
class MappingStar2PassTest extends AbstractTestMapping {
val aligner = "star-2pass"
}
class MappingBowtieTest extends AbstractTestMapping {
val aligner = "bowtie"
}
class MappingStampyTest extends AbstractTestMapping {
val aligner = "stampy"
}
class MappingGsnapTest extends AbstractTestMapping {
val aligner = "gsnap"
}
class MappingTophatTest extends AbstractTestMapping {
val aligner = "tophat"
}
object MappingTest {
val aligners = Array("bwa-mem", "bwa-aln", "star", "star-2pass", "bowtie", "stampy", "gsnap", "tophat")
val outputDir = Files.createTempDir()
new File(outputDir, "input").mkdirs()
......
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