Add relative symlink option to Ln wrapper

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala

 package nl.lumc.sasc.biopet.function
 
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.queue.function.InProcessFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 import scala.sys.process.Process
+import org.apache.commons.io.FilenameUtils;
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.core.config.Configurable
 
 class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   this.analysisName = getClass.getSimpleName
@@ -15,8 +16,61 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   @Output(doc = "Link destination")
   var out: File = _
 
+  var relative: Boolean = true
+
+  private lazy val inCanonical: String = {
+    // need to remove "/~" to correctly expand path with tilde
+    in.getCanonicalPath().replace("/~", "")
+  }
+
+  private lazy val outCanonical: String = {
+    out.getCanonicalPath().replace("/~", "")
+  }
+
+  private lazy val inToks: Array[String] = {
+    inCanonical.split(File.separator)
+  }
+
+  private lazy val outToks: Array[String] = {
+    outCanonical.split(File.separator)
+  }
+
+  private lazy val commonPrefixLength: Int = {
+    val maxLength = scala.math.min(inToks.length, outToks.length)
+    var i: Int = 0;
+    while (i < maxLength && inToks(i) == outToks(i)) i += 1;
+    i
+  }
+
+  private lazy val inUnique: String = {
+    inToks.slice(commonPrefixLength, inToks.length).mkString(File.separator)
+  }
+
+  private lazy val outUnique: String = {
+    outToks.slice(commonPrefixLength, outToks.length).mkString(File.separator)
+  }
+
+  private lazy val inRelative: String = {
+    // calculate 'distance' from output directory to input
+    // which is the number of directory walks required to get to the inUnique directory from outDir
+    val outDir = FilenameUtils.getFullPathNoEndSeparator(outUnique)
+    val dist: Int = scala.math.max(0, outDir.split(File.separator).length - 1)
+    val result =
+      if (dist > 0)
+        ((".." + File.separator) * dist) + File.separator + inUnique
+      else
+        inUnique
+    result
+  }
+
   override def run {
-    val cmd = "ln -s " + in + " " + out
+    val cmd =
+      if (relative) {
+        // workaround until we have `ln` that works with relative path (i.e. `ln -r`)
+        "ln -s " + inRelative + " " + outCanonical
+      } else {
+        "ln -s " + inCanonical + " " + outCanonical
+      }
     val process = Process(cmd).run
     System.out.println("cmd: '" + cmd + "', exitcode: " + process.exitValue)
   }