From a12e3ec3586be4a10135609ffed07f10142fef4f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Feb 2015 09:37:40 +0100
Subject: [PATCH] Fix typo bug
---
.../main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index e322b4673..6dd074621 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -207,9 +207,8 @@ object VcfStats extends ToolCommand {
val stats = createStats
logger.info("Starting on: " + interval)
- for (
- record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd) if record.getStart <= interval.getEnd
- ) {
+ for (record <- reader.query(interval.getSequence, interval.getStart, interval.getEnd)
+ if record.getStart <= interval.getEnd) {
mergeNestedStatsMap(stats.generalStats, checkGeneral(record))
for (sample1 <- samples) yield {
val genotype = record.getGenotype(sample1)
@@ -253,7 +252,7 @@ object VcfStats extends ToolCommand {
buffer += key -> (map + (value -> (map.getOrElse(value, 0) + 1)))
}
- buffer += "qual" -> Map(record.getPhredScaledQual -> 1)
+ buffer += "QUAL" -> Map(record.getPhredScaledQual -> 1)
addToBuffer("general", "Total")
if (record.isBiallelic) addToBuffer("general", "Biallelic")
--
GitLab