Spelling error

bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -7,7 +7,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.apps.{BedToInterval, BiopetFlagstat}
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.bedtools.{BedtoolsCoverage, BedtoolsIntersect}
-import nl.lumc.sasc.biopet.function.picard.{CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics}
+import nl.lumc.sasc.biopet.function.picard.{CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics}
 import nl.lumc.sasc.biopet.function.samtools.SamtoolsFlagstat
 
 class BamMetrics(val root:Configurable) extends QScript with BiopetQScript {
@@ -36,6 +36,7 @@ class BamMetrics(val root:Configurable) extends QScript with BiopetQScript {
     add(BiopetFlagstat(this, inputBam, outputDir))
     add(CollectGcBiasMetrics(this, inputBam, outputDir))
     add(CollectInsertSizeMetrics(this, inputBam, outputDir))
+    add(CollectAlignmentSummaryMetrics(this, inputBam, outputDir))
     
     val baitIntervalFile = if (baitBedFile != null) new File(outputDir, baitBedFile.getName.stripSuffix(".bed") + ".interval") else null
     if (baitIntervalFile != null)

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

@@ -22,8 +22,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   var vmem: String = _
   val defaultVmem: String = ""
   
-  @Argument(doc="Executeble")
-  var executeble: String = _
+  @Argument(doc="Executable")
+  var executable: String = _
   
   protected def beforeCmd {
   }
@@ -32,7 +32,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   }
   
   override def freezeFieldValues() {
-    checkExecuteble
+    checkExecutable
     afterGraph
     jobOutputFile = new File(firstOutput.getParent + "/."  + firstOutput.getName + "." + analysisName + ".out")
     
@@ -49,26 +49,26 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     super.freezeFieldValues()
   }
   
-  protected def checkExecuteble {
-    try if (executeble != null) {
+  protected def checkExecutable {
+    try if (executable != null) {
       val buffer = new StringBuffer()
-      val cmd = Seq("which", executeble)
+      val cmd = Seq("which", executable)
       val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
       if (process.exitValue == 0) {
-        executeble = buffer.toString
-        val file = new File(executeble)
-        executeble = file.getCanonicalPath
+        executable = buffer.toString
+        val file = new File(executable)
+        executable = file.getCanonicalPath
       } else {
-        logger.error("executeble: '" + executeble + "' not found, please check config")
-        throw new QException("executeble: '" + executeble + "' not found, please check config")
+        logger.error("executable: '" + executable + "' not found, please check config")
+        throw new QException("executable: '" + executable + "' not found, please check config")
       }
     } catch {
-      case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executeble skipped: " + ioe)
+      case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
     }
   }
   
   final protected def preCmdInternal {
-    checkExecuteble
+    checkExecutable
     //for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
     //logger.debug("Config for " + analysisName + ": " + localConfig)
     
@@ -96,7 +96,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
         case _ =>
       }
     }
-    logger.warn("Version command: '" + versionCommand + "' give a exit code " + process.exitValue + " but no version was found, executeble oke?")
+    logger.warn("Version command: '" + versionCommand + "' give a exit code " + process.exitValue + " but no version was found, executable oke?")
     return "N/A"
   }
   

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

@@ -3,12 +3,12 @@ package nl.lumc.sasc.biopet.core
 import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 
 abstract class BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
-  executeble = "java"
+  executable = "java"
   
   override def commandLine: String = {
     preCmdInternal
     val cmd = super.commandLine
-    val finalCmd = executeble + cmd.substring(cmd.indexOf(" "))
+    val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
 //    addJobReportBinding("command", cmd)
     return cmd
   }

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

@@ -12,9 +12,9 @@ class Cat(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="Unzipped file", required=true)
   var output: File = _
   
-  executeble = config("exe", "cat")
+  executable = config("exe", "cat")
   
-  def cmdLine = required(executeble) + repeat(input) + " > " + required(output)
+  def cmdLine = required(executable) + repeat(input) + " > " + required(output)
 }
 
 object Cat {

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

@@ -13,7 +13,7 @@ class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="Unzipped file")
   var output: File = _
   
-  executeble = config("exe", "pbzip2")
+  executable = config("exe", "pbzip2")
   
   var decomrpess = true
   var memory: Int = config("memory", 1000)
@@ -25,7 +25,7 @@ class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {
     memory = memory * threads
   }
   
-  def cmdLine = required(executeble) +
+  def cmdLine = required(executable) +
       conditional(decomrpess, "-d") +
       conditional(!decomrpess, "-z") +
       optional("-p", threads, spaceSeparated=false) +

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

@@ -10,7 +10,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
   @Input(doc="Python script", required=false)
   var python_script: File = _
   
-  executeble = config("python_exe", "python")
+  executable = config("python_exe", "python")
   
   protected var python_script_name : String = _
   def setPythonScript(script:String) { setPythonScript(script,"") }
@@ -25,6 +25,6 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
   }
   
   def getPythonCommand() : String = {
-    required(executeble) + required(python_script)
+    required(executable) + required(python_script)
   }
 }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala

@@ -12,7 +12,7 @@ class Sha1sum(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="Unzipped file")
   var output: File = _
   
-  executeble = config("exe","sha1sum")
+  executable = config("exe","sha1sum")
   
-  def cmdLine = required(executeble) + required(input) + " > " + required(output)
+  def cmdLine = required(executable) + required(input) + " > " + required(output)
 }
\ No newline at end of file

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

@@ -12,9 +12,9 @@ class Zcat(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="Unzipped file")
   var output: File = _
   
-  executeble = config("exe", "zcat")
+  executable = config("exe", "zcat")
   
-  def cmdLine = required(executeble) + required(input) + " > " + required(output)
+  def cmdLine = required(executable) + required(input) + " > " + required(output)
 }
 
 object Zcat {

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

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.function.bedtools
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 abstract class Bedtools extends BiopetCommandLineFunction {
-  executeble = config("exe", "bedtools", "bedtools")
-  override def versionCommand = executeble + " --version"
+  executable = config("exe", "bedtools", "bedtools")
+  override def versionCommand = executable + " --version"
   override val versionRegex = """bedtools (.*)""".r
 }
\ No newline at end of file

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

@@ -23,7 +23,7 @@ class BedtoolsCoverage(val root:Configurable) extends Bedtools {
     if (input.getName.endsWith(".bam")) inputTag = "-abam"
   }
   
-  def cmdLine = required(executeble) + required("coverage") + 
+  def cmdLine = required(executable) + required("coverage") + 
     required(inputTag, input) + 
     required("-b", intersectFile) + 
     conditional(depth, "-d") + 

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

@@ -26,7 +26,7 @@ class BedtoolsIntersect(val root:Configurable) extends Bedtools {
     if (input.getName.endsWith(".bam")) inputTag = "-abam"
   }
   
-  def cmdLine = required(executeble) + required("intersect") + 
+  def cmdLine = required(executable) + required("intersect") + 
     required(inputTag, input) + 
     required("-b", intersectFile) + 
     required("-f", minOverlap) + 

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

@@ -25,7 +25,7 @@ trait Picard extends BiopetJavaCommandLineFunction {
   @Argument(doc="CREATE_MD5_FILE", required = false)
   var createMd5: Boolean = config("createmd5", false, "picard")
   
-  override def versionCommand = executeble + " " + javaOpts + " " + javaExecutable + " -h"
+  override def versionCommand = executable + " " + javaOpts + " " + javaExecutable + " -h"
   override val versionRegex = """Version: (.*)""".r
   override val versionExitcode = List(0,1)
   

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

@@ -3,8 +3,8 @@ package nl.lumc.sasc.biopet.function.samtools
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 abstract class Samtools extends BiopetCommandLineFunction {
-  executeble = config("exe", "samtools", "samtools")
-  override def versionCommand = executeble
+  executable = config("exe", "samtools", "samtools")
+  override def versionCommand = executable
   override val versionRegex = """Version: (.*)""".r
   override val versionExitcode = List(0,1)
 }
\ No newline at end of file

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

@@ -11,7 +11,7 @@ class SamtoolsFlagstat(val root:Configurable) extends Samtools {
   @Output(doc="output File")
   var output: File = _
   
-  def cmdLine = required(executeble) + required("flagstat") + required(input) + " > " + required(output)
+  def cmdLine = required(executable) + required("flagstat") + required(input) + " > " + required(output)
 }
 
 object SamtoolsFlagstat {

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala

@@ -17,8 +17,8 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="Output fastq file")
   var fastq_output: File = _
   
-  executeble = config("exe","cutadapt")
-  override def versionCommand = executeble + " --version"
+  executable = config("exe","cutadapt")
+  override def versionCommand = executable + " --version"
   override val versionRegex = """(.*)""".r
   
   var default_clip_mode:String = config("default_clip_mode", "3")
@@ -37,7 +37,7 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
   def cmdLine = {
     if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
       analysisName = getClass.getName
-      required(executeble) +
+      required(executable) +
       // options
       repeat("-a", opt_adapter) + 
       repeat("-b", opt_anywhere) + 

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala

@@ -17,7 +17,7 @@ class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="Output", shortName="out")
   var output: File = _
   
-  executeble = config("exe","fastqc")
+  executable = config("exe","fastqc")
   var java_exe: String = config("exe", "java", "java")
   var kmers: Int = config("kmers", 5)
   var quiet: Boolean = config("quiet", false)
@@ -28,15 +28,15 @@ class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
   override val defaultThreads = 4
   
   override def afterGraph {
-    this.checkExecuteble
-    val fastqcDir = executeble.substring(0, executeble.lastIndexOf("/"))
+    this.checkExecutable
+    val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
     if (contaminants == null) contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
   }
   
-  override def versionCommand = executeble + " --version"
+  override def versionCommand = executable + " --version"
   
   def cmdLine = {
-    required(executeble) + 
+    required(executable) + 
       optional("--java", java_exe) +
       optional("--threads",threads) +
       optional("--contaminants",contaminants) +

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala

@@ -29,7 +29,7 @@ class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="stats output")
   var output_stats: File = null
   
-  executeble = config("exe", "sickle")
+  executable = config("exe", "sickle")
   var qualityType: String = config("qualitytype", null)
   
   var defaultQualityType: String = _
@@ -40,14 +40,14 @@ class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
     if (qualityType == null && defaultQualityType != null) qualityType = defaultQualityType
   }
   
-  override def versionCommand = executeble + " --version"
+  override def versionCommand = executable + " --version"
   
   override def beforeCmd {
     qualityType = getQualityTypeFromFile
   }
   
   def cmdLine = {
-    var cmd: String = required(executeble)
+    var cmd: String = required(executable)
     if (input_R2 != null) {
       cmd += required("pe") +
       required("-r", input_R2) + 

mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala

@@ -22,17 +22,17 @@ class Bwa(val root:Configurable) extends BiopetCommandLineFunction {
   var RG: String = _
   var M: Boolean = config("M", true)
   
-  executeble = config("exe", "bwa")
+  executable = config("exe", "bwa")
   override val versionRegex = """Version: (.*)""".r
   override val versionExitcode = List(0,1)
   
   override val defaultVmem = "6G"
   override val defaultThreads = 8
   
-  override def versionCommand = executeble
+  override def versionCommand = executable
   
   def cmdLine = {
-    required(executeble) + 
+    required(executable) + 
     required("mem") + 
     optional("-t", nCoresRequest) + 
     optional("-R", RG) + 

mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala

@@ -34,7 +34,7 @@ class Star(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="Output SAindex file", required=false)
   var outputSAindex: File = _
   
-  executeble = config("exe", "STAR")
+  executable = config("exe", "STAR")
   
   @Argument(doc="Output Directory")
   var outputDir: String = _
@@ -64,7 +64,7 @@ class Star(val root:Configurable) extends BiopetCommandLineFunction {
   }
   
   def cmdLine : String = {
-    var cmd: String = required("cd",outputDir) + "&&" + required(executeble)
+    var cmd: String = required("cd",outputDir) + "&&" + required(executable)
     if (runmode != null && runmode == "genomeGenerate") { // Create index
       cmd += required("--runMode", runmode) +
         required("--genomeFastaFiles", referenceFile)