From a5afc3e55b50a7303e2bb834237c8c75118914be Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 30 Mar 2016 20:26:10 +0200
Subject: [PATCH] Switch back to vcf 4.1
---
.../main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index cde91a20e..a9eef0016 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -66,7 +66,7 @@ object MpileupToVcf extends ToolCommand {
if (commandArgs.input != null && !commandArgs.input.exists) throw new IllegalStateException("Input file does not exist")
val writer = new PrintWriter(commandArgs.output)
- writer.println("##fileformat=VCFv4.2")
+ writer.println("##fileformat=VCFv4.1")
writer.println("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">")
writer.println("##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">")
writer.println("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">")
@@ -76,7 +76,7 @@ object MpileupToVcf extends ToolCommand {
writer.println("##FORMAT=<ID=RRC,Number=1,Type=Integer,Description=\"Reference Reverse Reads\">")
writer.println("##FORMAT=<ID=AFC,Number=A,Type=Integer,Description=\"Alternetive Forward Reads\">")
writer.println("##FORMAT=<ID=ARC,Number=A,Type=Integer,Description=\"Alternetive Reverse Reads\">")
- writer.println("##FORMAT=<ID=SEQ-ERR,Number=R,Type=Float,Description=\"Probilty to not be a sequence error with error rate " + commandArgs.seqError + "\">")
+ writer.println("##FORMAT=<ID=SEQ-ERR,Number=.,Type=Float,Description=\"Probilty to not be a sequence error with error rate " + commandArgs.seqError + "\">")
writer.println("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">")
writer.println("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" + commandArgs.sample)
val inputStream = if (commandArgs.input != null) {
--
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