Merge branch 'fix-reference_dict_check' into 'develop'

Extract checkDict and checkFai in a public method

Fix for #173

Still needs testing.

See merge request !190

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -15,15 +15,16 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
 
   jarFile = config("gatk_jar")
 
-  override val defaultCoreMemory = 4.0
+  override def defaultCoreMemory = 4.0
+  override def faiRequired = true
 
   if (config.contains("intervals")) intervals = config("intervals").asFileList
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree")
 
-  override val versionRegex = """(.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """(.*)""".r
+  override def versionExitcode = List(0, 1)
   override def versionCommand = executable + " -jar " + jarFile + " -version"
 
   override def getVersion = super.getVersion.collect { case version => "Gatk " + version }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

@@ -33,11 +33,11 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   var deps: List[File] = Nil
 
   var threads = 0
-  val defaultThreads = 1
+  def defaultThreads = 1
 
   var vmem: Option[String] = config("vmem")
-  protected val defaultCoreMemory: Double = 1.0
-  protected val defaultVmemFactor: Double = 1.4
+  protected def defaultCoreMemory: Double = 1.0
+  protected def defaultVmemFactor: Double = 1.4
   var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
 
   var residentFactor: Double = config("resident_factor", default = 1.2)
@@ -151,10 +151,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   protected def versionCommand: String = null
 
   /** Regex to get version from version command output */
-  protected val versionRegex: Regex = null
+  protected def versionRegex: Regex = null
 
   /** Allowed exit codes for the version command */
-  protected val versionExitcode = List(0)
+  protected def versionExitcode = List(0)
 
   /** Executes the version command */
   private[core] def getVersionInternal(): Option[String] = {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

@@ -25,7 +25,7 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
   javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
   javaGCTimeLimit = config("java_gc_timelimit")
 
-  override protected val defaultVmemFactor: Double = 2.0
+  override protected def defaultVmemFactor: Double = 2.0
 
   /** Constructs java opts, this adds scala threads */
   override def javaOpts = super.javaOpts +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

@@ -59,6 +59,7 @@ trait Reference extends Configurable {
 
   /** Create summary part for reference */
   def referenceSummary: Map[String, Any] = {
+    Reference.requireDict(referenceFasta())
     val file = new IndexedFastaSequenceFile(referenceFasta())
     Map("contigs" ->
       (for (seq <- file.getSequenceDictionary.getSequences) yield seq.getSequenceName -> {
@@ -77,16 +78,8 @@ trait Reference extends Configurable {
     if (!Reference.checked.contains(file)) {
       require(file.exists(), "Reference not found: " + file)
 
-      if (dictRequired) {
-        val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
-        require(dict.exists(), "Reference is missing a dict file")
-      }
-
-      if (faiRequired) {
-        val fai = new File(file.getAbsolutePath + ".fai")
-        require(fai.exists(), "Reference is missing a fai file")
-        require(IndexedFastaSequenceFile.canCreateIndexedFastaReader(file), "Index of reference cannot be loaded, reference: " + file)
-      }
+      if (dictRequired) Reference.requireDict(file)
+      if (faiRequired) Reference.requireFai(file)
 
       Reference.checked += file
     }
@@ -97,4 +90,26 @@ object Reference {
 
   /** Used as cache to avoid double checking */
   private var checked: Set[File] = Set()
+
+  /**
+   * Raise an exception when given fasta file has no fai file
+   * @param fastaFile Fasta file
+   * @throws IllegalArgumentException
+   */
+  def requireFai(fastaFile: File): Unit = {
+    val fai = new File(fastaFile.getAbsolutePath + ".fai")
+    require(fai.exists(), "Reference is missing a fai file")
+    require(IndexedFastaSequenceFile.canCreateIndexedFastaReader(fastaFile),
+      "Index of reference cannot be loaded, reference: " + fastaFile)
+  }
+
+  /**
+   * Raise an exception when given fasta file has no dict file
+   * @param fastaFile Fasta file
+   * @throws IllegalArgumentException
+   */
+  def requireDict(fastaFile: File): Unit = {
+    val dict = new File(fastaFile.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+    require(dict.exists(), "Reference is missing a dict file")
+  }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -26,7 +26,7 @@ trait ReportBuilderExtension extends ToolCommandFuntion {
   /** Arguments that are passed on the commandline */
   var args: Map[String, String] = Map()
 
-  override val defaultCoreMemory = 3.0
+  override def defaultCoreMemory = 3.0
 
   override def beforeGraph: Unit = {
     super.beforeGraph

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

@@ -40,12 +40,12 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
   var output: File = null
 
   executable = config("exe", default = "bowtie", freeVar = false)
-  override val versionRegex = """.*[Vv]ersion:? (.*)""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """.*[Vv]ersion:? (.*)""".r
+  override def versionExitcode = List(0, 1)
   override def versionCommand = executable + " --version"
 
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 8
 
   var sam: Boolean = config("sam", default = true)
   var sam_RG: Option[String] = config("sam-RG")

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

@@ -30,10 +30,10 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "cufflinks")
 
   /** default threads */
-  override val defaultThreads = 8
+  override def defaultThreads = 8
 
   /** default vmem for cluster jobs */
-  override val defaultCoreMemory = 6.0
+  override def defaultCoreMemory = 6.0
 
   /** input file */
   @Input(doc = "Input file (SAM or BAM)", required = true)
@@ -184,9 +184,9 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   /** do not contact server to check for update availability [FALSE] */
   var no_update_check: Boolean = config("no_update_check", default = false)
 
-  override val versionRegex = """cufflinks v(.*)""".r
+  override def versionRegex = """cufflinks v(.*)""".r
   override def versionCommand = executable
-  override val versionExitcode = List(0, 1)
+  override def versionExitcode = List(0, 1)
 
   def cmdLine =
     required(executable) +

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

@@ -117,9 +117,9 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction {
   /** Disable SCV correction */
   var no_scv_correction: Boolean = config("no_scv_correction", default = false)
 
-  override val versionRegex = """cuffquant v(.*)""".r
+  override def versionRegex = """cuffquant v(.*)""".r
   override def versionCommand = executable
-  override val versionExitcode = List(0, 1)
+  override def versionExitcode = List(0, 1)
 
   def cmdLine =
     required(executable) +

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

@@ -40,7 +40,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
 
   executable = config("exe", default = "cutadapt")
   override def versionCommand = executable + " --version"
-  override val versionRegex = """(.*)""".r
+  override def versionRegex = """(.*)""".r
 
   var default_clip_mode: String = config("default_clip_mode", default = "3")
   var opt_adapter: Set[String] = config("adapter", default = Nil)

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

@@ -48,9 +48,9 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   var nogroup: Boolean = config("nogroup", default = false)
   var extract: Boolean = config("extract", default = true)
 
-  override val versionRegex = """FastQC (.*)""".r
+  override def versionRegex = """FastQC (.*)""".r
   override def versionCommand = executable + " --version"
-  override val defaultThreads = 4
+  override def defaultThreads = 4
 
   /** Sets contaminants and adapters when not yet set */
   override def beforeGraph {

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

@@ -39,7 +39,7 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
   var haplotypeLength: Option[Int] = config("haplotype_length")
 
   executable = config("exe", default = "freebayes")
-  override val versionRegex = """version:  (.*)""".r
+  override def versionRegex = """version:  (.*)""".r
   override def versionCommand = executable + " --version"
 
   override def beforeGraph: Unit = {

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

@@ -32,10 +32,10 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
   executable = config("exe", default = "gsnap", freeVar = false)
 
   /** default threads */
-  override val defaultThreads = 8
+  override def defaultThreads = 8
 
   /** default vmem for cluster jobs */
-  override val defaultCoreMemory = 10.0
+  override def defaultCoreMemory = 10.0
 
   /** input file */
   @Input(doc = "Input FASTQ file(s)", required = true) //var input: List[File] = _
@@ -329,7 +329,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
   /** value to put into read-group library (rg-pl) field */
   var read_group_platform: Option[String] = config("read_group_platform")
 
-  override val versionRegex = """.* version (.*)""".r
+  override def versionRegex = """.* version (.*)""".r
   override def versionCommand = executable + " --version"
 
   def cmdLine = {

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

@@ -29,7 +29,7 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "gzip")
 
-  override val versionRegex = """gzip (.*)""".r
+  override def versionRegex = """gzip (.*)""".r
   override def versionCommand = executable + " --version"
 
   def cmdLine = required(executable) + " -c " + repeat(input) + " > " + required(output)

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

@@ -69,7 +69,7 @@ class HtseqCount(val root: Configurable) extends BiopetCommandLineFunction {
   /** suppress progress report */
   var quiet: Boolean = config("quiet", default = false)
 
-  override val versionRegex = """.*, version (.*)\.""".r
+  override def versionRegex = """.*, version (.*)\.""".r
   override def versionCommand = executable + " --help"
 
   def cmdLine = {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala

@@ -33,7 +33,7 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "md5sum")
 
-  override val versionRegex = """md5sum \(GNU coreutils\) (.*)""".r
+  override def versionRegex = """md5sum \(GNU coreutils\) (.*)""".r
   override def versionCommand = executable + " --version"
 
   /** return commandline to execute */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala

@@ -33,8 +33,8 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
   var decomrpess = true
   var memory: Option[Int] = config("memory")
 
-  override val defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
-  override val defaultThreads = 2
+  override def defaultCoreMemory = memory.getOrElse(1000).toDouble / 1000
+  override def defaultThreads = 2
 
   override def beforeCmd {
     if (!memory.isEmpty) memory = Option(memory.get * threads)

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

@@ -27,9 +27,9 @@ import scalaz.std.boolean.option
  */
 class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
 
-  override val defaultThreads = 1
+  override def defaultThreads = 1
   override def versionCommand = executable + " -v"
-  override val versionRegex = """.*version ([\w\.]*) .*""".r
+  override def versionRegex = """.*version ([\w\.]*) .*""".r
 
   @Input(doc = "Input phy/fasta file", required = true)
   var input: File = _

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

@@ -58,7 +58,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
   var discardN: Boolean = config("discardN", default = false)
   var quiet: Boolean = config("quiet", default = false)
   var defaultQualityType: String = config("defaultqualitytype", default = "sanger")
-  override val versionRegex = """sickle version (.*)""".r
+  override def versionRegex = """sickle version (.*)""".r
   override def versionCommand = executable + " --version"
 
   /** Sets qualityType is still empty */

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

@@ -60,12 +60,12 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction with Refe
   var logfile: Option[String] = config("logfile")
 
   executable = config("exe", default = "stampy.py", freeVar = false)
-  override val versionRegex = """stampy v(.*) \(.*\), .*""".r
-  override val versionExitcode = List(0, 1)
+  override def versionRegex = """stampy v(.*) \(.*\), .*""".r
+  override def versionExitcode = List(0, 1)
 
   /// Stampy uses approx factor 1.1 times the size of the genome in memory.
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 8
 
   override def versionCommand = executable + " --help"
 

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

@@ -63,8 +63,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
   var outFileNamePrefix: String = _
   var runThreadN: Option[Int] = config("runThreadN")
 
-  override val defaultCoreMemory = 4.0
-  override val defaultThreads = 8
+  override def defaultCoreMemory = 4.0
+  override def defaultThreads = 8
 
   /** Sets output files for the graph */
   override def beforeGraph() {