Changed output of stats for coverage stats

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

@@ -156,6 +156,8 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
       //FIXME:should use piping
       add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true), true)
       val covStats = CoverageStats(this, coverageFile, targetDir)
+      covStats.title = Some("Coverage for " + targetName)
+      covStats.subTitle = Some(" ")
       add(covStats)
       addSummarizable(covStats, "cov_stats")
     }

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py

@@ -318,14 +318,4 @@ if __name__ == '__main__':
                 title=title, out_img=args.plot)
 
     stats = {'coverage': {k: v.get_quick_stats() for k, v in coverages.items()}}
-    if args.plot is not None:
-        files = {'plot_coverage': {
-            'path': os.path.abspath(args.plot),
-            'checksum_sha1': None,
-            }
-        }
-    else:
-        files = {}
-
-    json.dump({'stats': stats, 'files': files}, sys.stdout, sort_keys=True, indent=4,
-            separators=(',', ': '))
\ No newline at end of file
+    json.dump(stats, sys.stdout, sort_keys=True, indent=4, separators=(',', ': '))
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.scripts
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
@@ -33,14 +34,23 @@ class CoverageStats(val root: Configurable) extends PythonCommandLineFunction wi
   @Output(doc = "plot File (png)")
   var plot: File = _
 
+  var title: Option[String] = None
+  var subTitle: Option[String] = None
+
   override val defaultCoreMemory = 9.0
 
   def cmdLine = getPythonCommand +
-    required(input) + required("--plot", plot) + " > " + required(output)
+    required(input) +
+    required("--plot", plot) +
+    optional("--title", title) +
+    optional("--subtitle", subTitle) +
+    " > " + required(output)
 
   def summaryFiles: Map[String, File] = Map("output" -> output, "plot" -> plot)
 
-  def summaryStats: Map[String, Any] = Map()
+  def summaryStats: Map[String, Any] = {
+    ConfigUtils.fileToConfigMap(output)
+  }
 }
 
 object CoverageStats {

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

@@ -24,12 +24,12 @@ object ShivaReport extends MultisampleReportBuilder {
     val regions = regionsPage
     ReportPage(
       Map("Samples" -> generateSamplesPage(pageArgs)) ++
-      (if (regions.isDefined) Map(regions.get) else Map()) ++
-      Map("Files" -> filesPage,
-      "Versions" -> ReportPage(Map(), List((
-        "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-        ))), Map())
-      ),
+        (if (regions.isDefined) Map(regions.get) else Map()) ++
+        Map("Files" -> filesPage,
+          "Versions" -> ReportPage(Map(), List((
+            "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+            ))), Map())
+        ),
       List(
         "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
         "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",