Added some picard metrics to summary

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -62,10 +62,21 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 
   def biopetScript() {
     add(SamtoolsFlagstat(this, inputBam, swapExt(outputDir, inputBam, ".bam", ".flagstat")))
-    add(BiopetFlagstat(this, inputBam, swapExt(outputDir, inputBam, ".bam", ".biopetflagstat")))
+
+    val biopetFlagstat = BiopetFlagstat(this, inputBam, swapExt(outputDir, inputBam, ".bam", ".biopetflagstat"),
+      swapExt(outputDir, inputBam, ".bam", ".biopetflagstat.json"))
+    add(biopetFlagstat)
+    addSummarizable(biopetFlagstat, "biopet_flagstat")
+
     add(CollectGcBiasMetrics(this, inputBam, outputDir))
-    add(CollectInsertSizeMetrics(this, inputBam, outputDir))
-    add(CollectAlignmentSummaryMetrics(this, inputBam, outputDir))
+
+    val collectInsertSizeMetrics = CollectInsertSizeMetrics(this, inputBam, outputDir)
+    add(collectInsertSizeMetrics)
+    addSummarizable(collectInsertSizeMetrics, "insert_size_metrics")
+
+    val collectAlignmentSummaryMetrics = CollectAlignmentSummaryMetrics(this, inputBam, outputDir)
+    add(collectAlignmentSummaryMetrics)
+    addSummarizable(collectAlignmentSummaryMetrics, "alignment_metrics")
 
     val baitIntervalFile = if (baitBedFile != null) new File(outputDir, baitBedFile.getName.stripSuffix(".bed") + ".interval") else null
     if (baitIntervalFile != null)
@@ -81,12 +92,14 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
       val strictOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam")
       add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default = 1.0)), true)
       add(SamtoolsFlagstat(this, strictOutputBam, swapExt(targetDir, strictOutputBam, ".bam", ".flagstat")))
-      add(BiopetFlagstat(this, strictOutputBam, swapExt(targetDir, strictOutputBam, ".bam", ".biopetflagstat")))
+      add(BiopetFlagstat(this, strictOutputBam, swapExt(targetDir, strictOutputBam, ".bam", ".biopetflagstat"),
+        swapExt(targetDir, strictOutputBam, ".bam", ".biopetflagstat.json")))
 
       val looseOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam")
       add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default = 0.01)), true)
       add(SamtoolsFlagstat(this, looseOutputBam, swapExt(targetDir, looseOutputBam, ".bam", ".biopet")))
-      add(BiopetFlagstat(this, looseOutputBam, swapExt(targetDir, looseOutputBam, ".bam", ".biopetflagstat")))
+      add(BiopetFlagstat(this, looseOutputBam, swapExt(targetDir, looseOutputBam, ".bam", ".biopetflagstat"),
+        swapExt(targetDir, looseOutputBam, ".bam", ".biopetflagstat.json")))
 
       val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
       add(BedtoolsCoverage(this, inputBam, bedFile, coverageFile, true), true)

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

@@ -17,9 +17,10 @@ package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
-class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard {
+class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
   javaMainClass = "picard.analysis.CollectAlignmentSummaryMetrics"
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
@@ -59,6 +60,18 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard {
     optional("ASSUME_SORTED=", assumeSorted, spaceSeparated = false) +
     optional("STOP_AFTER=", stopAfter, spaceSeparated = false) +
     repeat("ADAPTER_SEQUENCE=", adapterSequence, spaceSeparated = false)
+
+  def summaryFiles: Map[String, File] = Map()
+
+  def summaryData: Map[String, Any] = {
+    val (header, content) = Picard.getMetrics(output)
+
+    (for (category <- 0 to content.size) yield {
+      content(category)(0) -> (for (i <- 1 to header.size) yield {
+        header(i).toLowerCase -> content(category)(i)
+      }).toMap
+    }).toMap
+  }
 }
 
 object CollectAlignmentSummaryMetrics {

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

@@ -17,11 +17,12 @@ package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 import scala.collection.immutable.Nil
 
-class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
+class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable {
   javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
@@ -31,7 +32,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
   var output: File = _
 
   @Output(doc = "Output histogram", required = true)
-  var outputHistogram: File = _
+  def outputHistogram: File = new File(output + ".pdf")
 
   @Argument(doc = "Reference file", required = false)
   var reference: File = config("reference")
@@ -55,7 +56,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
   var histogramWidth: Option[Int] = config("histogramWidth")
 
   override def beforeGraph {
-    if (outputHistogram == null) outputHistogram = new File(output + ".pdf")
+    //if (outputHistogram == null) outputHistogram = new File(output + ".pdf")
     //require(reference.exists)
   }
 
@@ -69,6 +70,14 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
     optional("STOP_AFTER=", stopAfter, spaceSeparated = false) +
     optional("HISTOGRAM_WIDTH=", histogramWidth, spaceSeparated = false) +
     conditional(assumeSorted, "ASSUME_SORTED=TRUE")
+
+  def summaryFiles: Map[String, File] = Map("output_histogram" -> outputHistogram)
+
+  def summaryData: Map[String, Any] = {
+    val (header, content) = Picard.getMetrics(output)
+    (for (i <- 0 to header.size)
+      yield (header(i).toLowerCase -> content.head(i))).toMap
+  }
 }
 
 object CollectInsertSizeMetrics {

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

@@ -15,9 +15,13 @@
  */
 package nl.lumc.sasc.biopet.extensions.picard
 
+import java.io.File
+
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument }
 
+import scala.io.Source
+
 abstract class Picard extends BiopetJavaCommandLineFunction {
   override def subPath = "picard" :: super.subPath
 
@@ -42,6 +46,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
   @Argument(doc = "CREATE_MD5_FILE", required = false)
   var createMd5: Boolean = config("createmd5", default = false)
 
+  //FIXME: picard version
   //  override def versionCommand = executable + " " + javaOpts + " " + javaExecutable + " -h"
   //  override val versionRegex = """Version: (.*)""".r
   //  override val versionExitcode = List(0, 1)
@@ -59,3 +64,17 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
     conditional(createIndex, "CREATE_INDEX=TRUE") +
     conditional(createMd5, "CREATE_MD5_FILE=TRUE")
 }
+
+object Picard {
+  def getMetrics(file: File) = {
+    val lines = Source.fromFile(file).getLines().toArray
+
+    val start = lines.indexWhere(_.startsWith("## METRICS CLASS")) + 1
+    val end = lines.indexOf("", start)
+
+    val header = lines(start).split("\t")
+    val content = (for (i <- (start + 1) until end) yield lines(i).split("\t")).toList
+
+    (header, content)
+  }
+}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

@@ -16,15 +16,16 @@
 package nl.lumc.sasc.biopet.tools
 
 import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
-import java.io.File
+import java.io.{ PrintWriter, File }
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import nl.lumc.sasc.biopet.core.ToolCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.collection.JavaConversions._
-import scala.collection.mutable.Map
 
-class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input bam", shortName = "input", required = true)
@@ -33,29 +34,44 @@ class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFuncti
   @Output(doc = "Output flagstat", shortName = "output", required = true)
   var output: File = _
 
+  @Output(doc = "summary output file", shortName = "output", required = false)
+  var summaryFile: File = _
+
   override val defaultVmem = "8G"
   memoryLimit = Option(4.0)
 
-  override def commandLine = super.commandLine + required("-I", input) + " > " + required(output)
+  override def commandLine = super.commandLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
+
+  def summaryFiles: Map[String, File] = Map()
+
+  def summaryData: Map[String, Any] = {
+    ConfigUtils.fileToConfigMap(summaryFile)
+  }
 }
 
 object BiopetFlagstat extends ToolCommand {
-  def apply(root: Configurable, input: File, output: File): BiopetFlagstat = {
+  import scala.collection.mutable.Map
+
+  def apply(root: Configurable, input: File, output: File, summaryFile: File): BiopetFlagstat = {
     val flagstat = new BiopetFlagstat(root)
     flagstat.input = input
     flagstat.output = output
+    flagstat.summaryFile = summaryFile
     return flagstat
   }
 
-  case class Args(inputFile: File = null, region: Option[String] = None) extends AbstractArgs
+  case class Args(inputFile: File = null, summaryFile: Option[File] = None, 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")
+    } text ("input bam file")
+    opt[File]('s', "summaryFile") valueName ("<file>") action { (x, c) =>
+      c.copy(summaryFile = Some(x))
+    } text ("summary output file")
     opt[String]('r', "region") valueName ("<chr:start-stop>") action { (x, c) =>
       c.copy(region = Some(x))
-    } text ("out is a required file property")
+    }
   }
 
   /**
@@ -127,6 +143,14 @@ object BiopetFlagstat extends ToolCommand {
       flagstatCollector.loadRecord(record)
     }
 
+    commandArgs.summaryFile.foreach {
+      case file => {
+        val writer = new PrintWriter(file)
+        writer.println(flagstatCollector.summary)
+        writer.close()
+      }
+    }
+
     println(flagstatCollector.report)
   }
 
@@ -207,6 +231,14 @@ object BiopetFlagstat extends ToolCommand {
       return buffer.toString
     }
 
+    def summary: String = {
+      val map = (for (t <- 0 until names.size) yield {
+        names(t) -> totalCounts(t)
+      }).toMap
+
+      return ConfigUtils.mapToJson(map).spaces4
+    }
+
     def crossReport(fraction: Boolean = false): String = {
       val buffer = new StringBuilder