Merge branch 'small_fixes' into 'develop'

Small fixes

Fixes two small issues

1. Extra docs for target beds/regions of interest for Shiva
2. Fixes integer overflow on WGS coverage statistics for report (Size of human genome > 2^31 -1 bases)

See merge request !177

docs/pipelines/shiva.md

@@ -113,6 +113,8 @@ To view all possible config options please navigate to our Gitlab wiki page
 | shiva | use_analyze_covariates | Boolean | false | Analyze covariates during base recalibration step |
 | shiva | bam_to_fastq | Boolean | false | Convert bam files to fastq files |
 | shiva | correct_readgroups | Boolean | false | Attempt to correct read groups |
+| shiva | amplicon_bed | Path | Path to target bed file |
+| shiva | regions_of_interest | Array of paths | Array of paths to region of interest (e.g. gene panels) bed files |
 | vcffilter | min_sample_depth | Integer | 8 | Filter variants with at least x coverage |
 | vcffilter | min_alternate_depth | Integer | 2 | Filter variants with at least x depth on the alternate allele |
 | vcffilter | min_samples_pass | Integer | 1 | Minimum amount of samples which pass custom filter (requires additional flags) |

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

@@ -195,7 +195,7 @@ object BammetricsReport extends ReportBuilder {
       }
     }
 
-    var map: Map[Int, Map[String, Int]] = Map()
+    var map: Map[Int, Map[String, Long]] = Map()
 
     def fill(sample: String, lib: Option[String]): Unit = {
 
@@ -208,7 +208,7 @@ object BammetricsReport extends ReportBuilder {
         case (l: List[_], l2: List[_]) => {
           l.zip(l2).foreach(i => {
             val insertSize = i._1.toString.toInt
-            val count = i._2.toString.toInt
+            val count = i._2.toString.toLong
             val old = map.getOrElse(insertSize, Map())
             if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
             else map += insertSize -> (old + (sample -> count))