From 928b380a3d71342813686f1128a1866e7ded5644 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 18 Apr 2016 15:36:47 +0200
Subject: [PATCH] fix #329
---
.../nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
index bf52dbea4..44252a173 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
@@ -20,6 +20,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.tryToParseNumber
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.io.Source
@@ -85,7 +86,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFunction with Summariz
Map("info" -> (for (
line <- Source.fromFile(generalStats).getLines().toList.tail;
values = line.split("\t") if values.size >= 2 && !values(0).isEmpty
- ) yield values(0) -> values(1).toInt
+ ) yield values(0) -> tryToParseNumber(values(1))
).toMap)
}
@@ -101,7 +102,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFunction with Summariz
for (s <- 1 until data(0).size) {
val sample = data(0)(s)
val stats = Map("genotype" -> (for (f <- 1 until data.length) yield {
- data(f)(0) -> data(f)(s)
+ data(f)(0) -> tryToParseNumber(data(f)(s))
}).toMap)
val sum = new Summarizable {
--
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