From 4a4fa9beb5bc3c6450bba17e3f8cf5626cc55ab3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 4 Dec 2014 11:26:34 +0100
Subject: [PATCH] Added Qual filter option
---
.../scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 85b2e236f..e948c05e6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -51,6 +51,7 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
object VcfFilter extends ToolCommand {
case class Args(inputVcf: File = null,
outputVcf: File = null,
+ minQualscore: Option[Double] = None,
minSampleDepth: Int = -1,
minTotalDepth: Int = -1,
minAlternateDepth: Int = -1,
@@ -105,6 +106,9 @@ object VcfFilter extends ToolCommand {
opt[Unit]("filterNoCalls") unbounded () action { (x, c) =>
c.copy(filterNoCalls = true)
} text ("Filter when there are only no calls")
+ opt[Double]("minQualscore") unbounded () action { (x, c) =>
+ c.copy(minQualscore = Some(x))
+ } text ("Min qual score")
}
var commandArgs: Args = _
@@ -122,7 +126,8 @@ object VcfFilter extends ToolCommand {
writer.writeHeader(header)
for (record <- reader) {
- if (filterRefCalls(record) &&
+ if (minQualscore(record) &&
+ filterRefCalls(record) &&
filterNoCalls(record) &&
minTotalDepth(record) &&
minSampleDepth(record) &&
@@ -139,6 +144,11 @@ object VcfFilter extends ToolCommand {
writer.close
}
+ def minQualscore(record: VariantContext): Boolean = {
+ if (commandArgs.minQualscore.isEmpty) return true
+ record.getPhredScaledQual >= commandArgs.minQualscore.get
+ }
+
def filterRefCalls(record: VariantContext): Boolean = {
if (commandArgs.filterNoCalls) record.getGenotypes.exists(g => !g.isHomRef)
else true
--
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