Commit 448669b6 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

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
parents 94afd24c 31ee8b17
......@@ -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) |
......
......@@ -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))
......
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