Change bwa to bwa-mem

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -40,7 +40,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
   def this() = this(null)
 
   override def defaults = ConfigUtils.mergeMaps(Map(
-    "mapping" -> Map("skip_markduplicates" -> true, "aligner" -> "bwa")
+    "mapping" -> Map("skip_markduplicates" -> true, "aligner" -> "bwa-mem")
   ), super.defaults)
 
   def summaryFile = new File(outputDir, "Carp.summary.json")

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -57,7 +57,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
   protected var skipMetrics: Boolean = config("skip_metrics", default = false)
 
   /** Aligner */
-  protected var aligner: String = config("aligner", default = "bwa")
+  protected var aligner: String = config("aligner", default = "bwa-mem")
 
   /** Number of chunks, when not defined pipeline will automatic calculate number of chunks */
   protected var numberChunks: Option[Int] = config("number_chunks")
@@ -209,7 +209,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
       val outputBam = new File(chunkDir, outputName + ".bam")
       bamFiles :+= outputBam
       aligner match {
-        case "bwa"        => addBwaMem(R1, R2, outputBam, deps)
+        case "bwa-mem"    => addBwaMem(R1, R2, outputBam, deps)
         case "bwa-aln"    => addBwaAln(R1, R2, outputBam, deps)
         case "bowtie"     => addBowtie(R1, R2, outputBam, deps)
         case "gsnap"      => addGsnap(R1, R2, outputBam, deps)

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -47,7 +47,7 @@ class MappingTest extends TestNGSuite with Matchers {
 
   @DataProvider(name = "mappingOptions")
   def mappingOptions = {
-    val aligners = Array("bwa", "bwa-aln", "star", "star-2pass", "bowtie", "stampy", "gsnap", "tophat")
+    val aligners = Array("bwa-mem", "bwa-aln", "star", "star-2pass", "bowtie", "stampy", "gsnap", "tophat")
     val paired = Array(true, false)
     val chunks = Array(1, 5, 10, 100)
     val skipMarkDuplicates = Array(true, false)
@@ -99,7 +99,7 @@ class MappingTest extends TestNGSuite with Matchers {
     mapping.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipFlexiprep) 0 else if (paired) 2 else 1)
 
     //aligners
-    mapping.functions.count(_.isInstanceOf[BwaMem]) shouldBe ((if (aligner == "bwa") 1 else 0) * chunks)
+    mapping.functions.count(_.isInstanceOf[BwaMem]) shouldBe ((if (aligner == "bwa-mem") 1 else 0) * chunks)
     mapping.functions.count(_.isInstanceOf[BwaAln]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 2 else 1) else 0) * chunks)
     mapping.functions.count(_.isInstanceOf[BwaSampe]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 1 else 0) else 0) * chunks)
     mapping.functions.count(_.isInstanceOf[BwaSamse]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 0 else 1) else 0) * chunks)
@@ -109,7 +109,7 @@ class MappingTest extends TestNGSuite with Matchers {
 
     // Sort sam or replace readgroup
     val sort = aligner match {
-      case "bwa" | "bwa-aln" | "stampy" => "sortsam"
+      case "bwa-mem" | "bwa-aln" | "stampy" => "sortsam"
       case "star" | "star-2pass" | "bowtie" | "gsnap" | "tophat" => "replacereadgroups"
       case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
     }