Added Markduplicates to summary

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.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 MarkDuplicates(val root: Configurable) extends Picard {
+class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
   javaMainClass = "picard.sam.MarkDuplicates"
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
@@ -91,6 +92,22 @@ class MarkDuplicates(val root: Configurable) extends Picard {
     optional("SORTING_COLLECTION_SIZE_RATIO=", sortingCollectionSizeRatio, spaceSeparated = false) +
     optional("READ_NAME_REGEX=", readNameRegex, spaceSeparated = false) +
     optional("OPTICAL_DUPLICATE_PIXEL_DISTANCE=", opticalDuplicatePixelDistance, spaceSeparated = false)
+
+  def summaryFiles: Map[String, File] = Map()
+
+  def summaryStats: Map[String, Any] = {
+    val (header, content) = Picard.getMetrics(outputMetrics)
+
+    (for (category <- 0 until content.size) yield {
+      content(category)(0) -> (
+        for (
+          i <- 1 until header.size if i < content(category).size
+        ) yield {
+          header(i).toLowerCase -> content(category)(i)
+        }).toMap
+    }
+    ).toMap
+  }
 }
 object MarkDuplicates {
   def apply(root: Configurable, input: List[File], outputDir: String): MarkDuplicates = {

public/biopet-framework/src/test/resources/picard.dedup.metrics

+## htsjdk.samtools.metrics.StringHeader
+# picard.sam.MarkDuplicates INPUT=[/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/samples/8080_2#43/lib_8080_1/8080_2#43-8080_1.bam] OUTPUT=/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/samples/8080_2#43/lib_8080_1/8080_2#43-8080_1.dedup.bam METRICS_FILE=/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/samples/8080_2#43/lib_8080_1/8080_2#43-8080_1.dedup.metrics TMP_DIR=[/data/DIV5/SASC/project-049-SNPtypingbac/analysis/runs/sp/.queue/tmp] CREATE_INDEX=true    PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates REMOVE_DUPLICATES=false ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Wed Feb 18 17:32:02 CET 2015
+
+## METRICS CLASS	picard.sam.DuplicationMetrics
+LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
+8080_1	5238	603803	115660	1077	5760	26	0.010386	31586584
+
+## HISTOGRAM	java.lang.Double
+BIN	VALUE
+1.0	1.000043
+2.0	1.98115
+3.0	2.943681
+4.0	3.887988
+5.0	4.814414
+6.0	5.723299
+7.0	6.614976
+8.0	7.489769
+9.0	8.347998
+10.0	9.189977
+11.0	10.016015
+12.0	10.826412
+13.0	11.621464
+14.0	12.401463
+15.0	13.166693
+16.0	13.917434
+17.0	14.653961
+18.0	15.376541
+19.0	16.085441
+20.0	16.780918
+21.0	17.463226
+22.0	18.132615
+23.0	18.78933
+24.0	19.433611
+25.0	20.065693
+26.0	20.685806
+27.0	21.294179
+28.0	21.891032
+29.0	22.476584
+30.0	23.051049
+31.0	23.614637
+32.0	24.167554
+33.0	24.710002
+34.0	25.24218
+35.0	25.76428
+36.0	26.276495
+37.0	26.779012
+38.0	27.272014
+39.0	27.755681
+40.0	28.230191
+41.0	28.695716
+42.0	29.152426
+43.0	29.60049
+44.0	30.040069
+45.0	30.471325
+46.0	30.894416
+47.0	31.309496
+48.0	31.716716
+49.0	32.116227
+50.0	32.508172
+51.0	32.892697
+52.0	33.269941
+53.0	33.640042
+54.0	34.003135
+55.0	34.359354
+56.0	34.708828
+57.0	35.051684
+58.0	35.388049
+59.0	35.718046
+60.0	36.041794
+61.0	36.359412
+62.0	36.671016
+63.0	36.97672
+64.0	37.276636
+65.0	37.570873
+66.0	37.859539
+67.0	38.14274
+68.0	38.420578
+69.0	38.693155
+70.0	38.960572
+71.0	39.222925
+72.0	39.480311
+73.0	39.732823
+74.0	39.980554
+75.0	40.223595
+76.0	40.462034
+77.0	40.695958
+78.0	40.925453
+79.0	41.150602
+80.0	41.371489
+81.0	41.588193
+82.0	41.800794
+83.0	42.00937
+84.0	42.213996
+85.0	42.414748
+86.0	42.611699
+87.0	42.804921
+88.0	42.994484
+89.0	43.180458
+90.0	43.362911
+91.0	43.541909
+92.0	43.717518
+93.0	43.889802
+94.0	44.058824
+95.0	44.224645
+96.0	44.387327
+97.0	44.546929
+98.0	44.703508
+99.0	44.857123
+100.0	45.00783
+

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala

+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvan_thof on 2/19/15.
+ */
+class MarkDuplicatesTest extends TestNGSuite with Matchers {
+
+  @Test
+  def summaryData: Unit = {
+    val file = new File(Paths.get(getClass.getResource("/picard.dedup.metrics").toURI).toString)
+    val job = new MarkDuplicates(null)
+    job.outputMetrics = file
+
+    job.summaryStats
+  }
+}
\ No newline at end of file

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -96,7 +96,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
   def summaryFiles = Map()
 
-  def summarySettings = Map()
+  def summarySettings = Map(
+    "skip_metrics" -> skipMetrics,
+    "skip_flexiprep" -> skipFlexiprep,
+    "skip_markduplicates" -> skipMarkduplicates,
+    "aligner" -> aligner,
+    "chunking" -> chunking,
+    "numberChunks" -> numberChunks.getOrElse(1)
+  )
 
   def init() {
     require(outputDir != null, "Missing output directory on mapping module")
@@ -208,7 +215,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     var bamFile = bamFiles.head
     if (!skipMarkduplicates) {
       bamFile = new File(outputDir, outputName + ".dedup.bam")
-      add(MarkDuplicates(this, bamFiles, bamFile))
+      val md = MarkDuplicates(this, bamFiles, bamFile)
+      add(md)
+      addSummarizable(md, "mark_duplicates")
     } else if (skipMarkduplicates && chunking) {
       val mergeSamFile = MergeSamFiles(this, bamFiles, outputDir)
       add(mergeSamFile)