Add the "-K" option from bwa

fulcrumgenomics · Feb 10, 2020 · c842b96 · c842b96
1 parent a0a77fb
commit c842b96
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/tasks/src/main/scala/dagr/tasks/bwa/Bwa.scala b/tasks/src/main/scala/dagr/tasks/bwa/Bwa.scala
@@ -49,15 +49,16 @@ object Bwa extends Configuration {
                      mergeBamAlignmentMem: String = "2G",
                      fifoBufferMem: String = "512M",
                      processAltMappings: Boolean = false,
-                     orientation: PairOrientation = PairOrientation.FR
+                     orientation: PairOrientation = PairOrientation.FR,
+                     numFixedBases: Option[Int] = None
                     ): Pipe[SamOrBam,SamOrBam] = {
     val alt = PathUtil.pathTo(s"${ref}.alt")
     val doAlt = Files.exists(alt) && processAltMappings
     val fifoMem: Memory = Memory(fifoBufferMem)
 
     val samToFastq = SamToFastq(in=unmappedBam, out=Io.StdOut).requires(Cores(samToFastqCores), Memory(samToFastqMem))
     val fqBuffer   = new FifoBuffer[Fastq].requires(memory=fifoMem)
-    val bwaMem     = new BwaMem(fastq=Io.StdIn, ref=ref, minThreads=minThreads, maxThreads=maxThreads, memory=Memory(bwaMemMemory))
+    val bwaMem     = new BwaMem(fastq=Io.StdIn, ref=ref, numFixedBases=numFixedBases, minThreads=minThreads, maxThreads=maxThreads, memory=Memory(bwaMemMemory))
     val bwaBuffer  = new FifoBuffer[Sam].requires(memory=fifoMem)
     val altPipe    = if (doAlt) new BwaK8AltProcessor(altFile=alt) | new FifoBuffer[Sam].requires(memory=fifoMem) else Pipes.empty[Sam]
     val mergeBam   = new MergeBamAlignment(unmapped=unmappedBam, mapped=Io.StdIn, out=mappedBam, ref=ref, sortOrder=sortOrder, orientation=orientation)

diff --git a/tasks/src/main/scala/dagr/tasks/bwa/BwaMem.scala b/tasks/src/main/scala/dagr/tasks/bwa/BwaMem.scala
@@ -43,6 +43,7 @@ class BwaMem(fastq: PathToFastq = Io.StdIn,
              clippingPenalties: Option[(Int,Int)] = None,
              minScore: Option[Int] = None,
              smartPairing: Boolean = true,
+             numFixedBases: Option[Int] = None,
              minThreads: Int = 1,
              maxThreads: Int = 32,
              memory: Memory = Memory("8G")
@@ -64,6 +65,7 @@ class BwaMem(fastq: PathToFastq = Io.StdIn,
     gapExtensionPenalties.foreach { case (del, ins) => buffer.append("-E", s"$del,$ins") }
     clippingPenalties.foreach { case (five, three) => buffer.append("-L", s"$five,$three") }
     minScore.foreach(s => buffer.append("-T", s))
+    numFixedBases.foreach(n => buffer.append("-K", n))
 
     buffer.append(ref, fastq)
     out.foreach(f => buffer.append("> " + f))