From 9c0409f6e6736dfd71ae14745e57a50ea3858710 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Feb 2015 18:23:20 +0100
Subject: [PATCH] Change name
---
.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
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 b0d09de61..c90b4ed49 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
@@ -211,6 +211,7 @@ object VcfStats extends ToolCommand {
val usedAlleles = (for (allele <- genotype.getAlleles) yield record.getAlleleIndex(allele)).toList
+ addToBuffer("general", "Total")
if (genotype.isHet) addToBuffer("general", "Het")
if (genotype.isHetNonRef) addToBuffer("general", "HetNonRef")
if (genotype.isHom) addToBuffer("general", "Hom")
@@ -243,7 +244,7 @@ object VcfStats extends ToolCommand {
val file = new File(prefix + field + ".tsv")
file.getParentFile.mkdirs()
val writer = new PrintWriter(file)
- writer.println(samples.mkString("\t", "\t", ""))
+ writer.println(samples.mkString(field+"\t", "\t", ""))
val keySet = (for (sample <- samples) yield stats.samplesStats(sample).genotypeStats.getOrElse(field, Map[Any, Int]()).keySet).fold(Set[Any]())(_ ++ _)
for (key <- keySet.toList.sortWith(sortAnyAny(_, _))) {
val values = for (sample <- samples) yield stats.samplesStats(sample).genotypeStats.getOrElse(field, Map[Any, Int]()).getOrElse(key, 0)
--
GitLab