From d66701baf6f290dbb1d79c6b997516f0779e12c3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 31 Mar 2016 14:26:03 +0200
Subject: [PATCH] Fixed bug in vcffilter (cherry picked from commit f5f2787)
---
.../main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index d08b05c53..bc91cfc04 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -276,8 +276,10 @@ object VcfFilter extends ToolCommand {
* @return
*/
def minGenomeQuality(record: VariantContext, minGQ: Int, minSamplesPass: Int = 1): Boolean = {
- record.getGenotypes.count(x => if (!x.hasGQ) false
- else if (x.getGQ >= minGQ) true else false) >= minSamplesPass
+ record.getGenotypes.count(x =>
+ if (minGQ == 0) true
+ else if (!x.hasGQ) false
+ else if (x.getGQ >= minGQ) true else false) >= minSamplesPass
}
/**
--
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