Added scopts library and log4j to ToolCommands

biopet-framework/pom.xml

@@ -66,6 +66,11 @@
             <artifactId>algebird-core_2.10</artifactId>
             <version>0.8.1</version>
         </dependency>
+        <dependency>
+                <groupId>com.github.scopt</groupId>
+                <artifactId>scopt_2.10</artifactId>
+                <version>3.2.0</version>
+        </dependency>
     </dependencies>
     <build>
         <resources>

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

 package nl.lumc.sasc.biopet.core
 
-import org.broadinstitute.gatk.queue.util.Logging
-
-
-trait MainCommand extends Logging {
+trait MainCommand {
 
   lazy val name = this.getClass.getSimpleName
     .split("\\$").last

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

 package nl.lumc.sasc.biopet.core
 
+import org.broadinstitute.gatk.queue.util.Logging
 
-trait PipelineCommand extends MainCommand {
+trait PipelineCommand extends MainCommand with Logging {
 
   def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
 

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

+package nl.lumc.sasc.biopet.core
+
+import java.text.SimpleDateFormat
+import java.util.Calendar
+import org.apache.log4j.Logger
+import org.apache.log4j.WriterAppender
+import org.apache.log4j.helpers.DateLayout
+import org.apache.log4j.spi.LoggingEvent
+import java.text.DateFormat
+
+trait ToolCommand extends MainCommand {
+  abstract class AbstractArgs {
+  }
+  
+  abstract class AbstractOptParser extends scopt.OptionParser[Args](getClass.getSimpleName) {
+    head(getClass.getSimpleName)
+    opt[String]('l', "log") foreach { x =>
+        x.toLowerCase match {
+          case "debug" => logger.setLevel(org.apache.log4j.Level.DEBUG)
+          case "info" => logger.setLevel(org.apache.log4j.Level.INFO)
+          case "warn" => logger.setLevel(org.apache.log4j.Level.WARN)
+          case "error" => logger.setLevel(org.apache.log4j.Level.ERROR)
+          case _ =>
+        } } text("Log level") // TODO: add Enum to validation
+  }
+  
+  type Args <: AbstractArgs
+  type OptParser <: AbstractOptParser
+   
+  protected val logger = Logger.getLogger(this.getClass.getSimpleName.stripSuffix("$"))
+  logger.setLevel(org.apache.log4j.Level.INFO)
+  logger.addAppender(new WriterAppender(new DateLayout() {
+        val ignoresThrowable = false
+        def format(event:org.apache.log4j.spi.LoggingEvent): String = {
+          val calendar: Calendar = Calendar.getInstance
+          calendar.setTimeInMillis(event.getTimeStamp)
+          val formatter: SimpleDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
+          val formattedDate: String = formatter.format(calendar.getTime)
+          var logLevel = event.getLevel.toString
+          while (logLevel.size < 6) logLevel += " "
+          logLevel + " [" + formattedDate + "] [" + event.getLoggerName + "] " + event.getMessage + "\n"
+        }
+      }, sys.process.stderr))
+}
\ No newline at end of file

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

@@ -4,6 +4,7 @@ import htsjdk.samtools.SAMFileReader
 import htsjdk.samtools.SAMRecord
 import java.io.File
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.core.ToolCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import org.broadinstitute.gatk.queue.util.Logging
@@ -22,10 +23,10 @@ class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFuncti
   override val defaultVmem = "8G"
   memoryLimit = Option(4.0)
 
-  override def commandLine = super.commandLine + required(input) + " > " + required(output)
+  override def commandLine = super.commandLine + required("I", input) + " > " + required(output)
 }
 
-object BiopetFlagstat extends Logging {
+object BiopetFlagstat extends ToolCommand {
   def apply(root: Configurable, input: File, output: File): BiopetFlagstat = {
     val flagstat = new BiopetFlagstat(root)
     flagstat.input = input
@@ -38,12 +39,32 @@ object BiopetFlagstat extends Logging {
     flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat")
     return flagstat
   }
+  
+  case class Args (inputFile:File = null, region:Option[String] = None) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('I', "inputFile") required() valueName("<file>") action { (x, c) =>
+      c.copy(inputFile = x) } text("out is a required file property")
+    opt[String]('r', "region") valueName("<chr:start-stop>") action { (x, c) =>
+      c.copy(region = Some(x)) } text("out is a required file property")
+  }
+  
   /**
    * @param args the command line arguments
    */
   def main(args: Array[String]): Unit = {
-    val inputSam = new SAMFileReader(new File(args(0)))
-
+    val argsParser = new OptParser
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)    
+    
+    val inputSam = new SAMFileReader(commandArgs.inputFile)
+    val iterSam = if (commandArgs.region == None) inputSam.iterator else {
+      val regionRegex = """(.*):(.*)-(.*)""".r
+      commandArgs.region.get match {
+        case regionRegex(chr, start, stop) => inputSam.query(chr, start.toInt, stop.toInt, false)
+        case _ => sys.error("Region wrong format")
+      }
+    }
+    
     val flagstatCollector = new FlagstatCollector
     flagstatCollector.loadDefaultFunctions
     val m = 10
@@ -90,9 +111,9 @@ object BiopetFlagstat extends Logging {
       record.getReferenceIndex == record.getMateReferenceIndex)
     flagstatCollector.addFunction("Mate on other chr", record => record.getReadPairedFlag && record.getReferenceIndex != record.getMateReferenceIndex)
 
-    for (record <- inputSam.iterator) {
+    for (record <- iterSam) {
       if (flagstatCollector.readsCount % 1e6 == 0 && flagstatCollector.readsCount > 0)
-        System.err.println("Reads prosessed: " + flagstatCollector.readsCount)
+        logger.info("Reads prosessed: " + flagstatCollector.readsCount)
       flagstatCollector.loadRecord(record)
     }