Added faidx

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFaidx.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.samtools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+/** Extension for samtools flagstat */
+class SamtoolsFaidx(val root: Configurable) extends Samtools {
+  @Input(doc = "Bam File")
+  var input: File = _
+
+  @Output(doc = "output File")
+  private var _output: File = _
+
+  def output = _output
+
+  override def beforeGraph: Unit = {
+    _output = new File(input.getParentFile, input.getName + ".fai")
+  }
+
+  /** Returns command to execute */
+  def cmdLine = required(executable) + required("faidx") + required(input)
+}
+
+object SamtoolsFaidx {
+  def apply(root: Configurable, input: File): SamtoolsFaidx = {
+    val faidx = new SamtoolsFaidx(root)
+    faidx.input = input
+    faidx._output = new File(input.getParentFile, input.getName + ".fai")
+    faidx
+  }
+}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala

@@ -19,6 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.{PipelineCommand, BiopetQScript}
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
 import nl.lumc.sasc.biopet.extensions.{Zcat, Curl}
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
@@ -49,17 +50,20 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
           throw new IllegalArgumentException(s"No fasta_url found for $speciesName - $genomeName")).toString
 
           val genomeDir = new File(speciesDir, genomeName)
+          val fastaFile = new File(genomeDir, "reference.fa")
 
           val curl = new Curl(this)
           curl.url = fastaUrl
           if (fastaUrl.endsWith(".gz")) {
             curl.output = new File(genomeDir, "reference.fa.gz")
             curl.isIntermediate = true
-            add(Zcat(this, curl.output, new File(genomeDir, "reference.fa")))
-          } else curl.output = new File(genomeDir, "reference.fa")
+            add(Zcat(this, curl.output, fastaFile))
+          } else curl.output = fastaFile
           add(curl)
 
-          //TODO: fai
+          val faidx = SamtoolsFaidx(this, fastaFile)
+          add(faidx)
+
           //TODO: dict
 
         //TODO: other indexes