From e7ed7e5fe9ddc288db2725989caf3b463f9ed2c9 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Wed, 8 Apr 2015 16:52:35 +0200
Subject: [PATCH] camelCase for arguments in VcfFilter. See issue #153
---
docs/tools/VcfFilter.md | 2 +-
.../nl/lumc/sasc/biopet/tools/VcfFilter.scala | 24 +++++++++----------
2 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/docs/tools/VcfFilter.md b/docs/tools/VcfFilter.md
index 696784035..b9b88c9cc 100644
--- a/docs/tools/VcfFilter.md
+++ b/docs/tools/VcfFilter.md
@@ -42,7 +42,7 @@ Usage: VcfFilter [options]
Filter when there are only ref calls
--filterNoCalls
Filter when there are only no calls
- --minQualscore <value>
+ --minQualScore <value>
Min qual score
~~~
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 d765ab7a8..64c8963f2 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
@@ -59,14 +59,14 @@ object VcfFilter extends ToolCommand {
case class Args(inputVcf: File = null,
outputVcf: File = null,
invertedOutputVcf: Option[File] = None,
- minQualscore: Option[Double] = None,
+ minQualScore: Option[Double] = None,
minSampleDepth: Int = -1,
minTotalDepth: Int = -1,
minAlternateDepth: Int = -1,
minSamplesPass: Int = 0,
minBamAlternateDepth: Int = 0,
mustHaveVariant: List[String] = Nil,
- denovoInSample: String = null,
+ deNovoInSample: String = null,
diffGenotype: List[(String, String)] = Nil,
filterHetVarToHomVar: List[(String, String)] = Nil,
filterRefCalls: Boolean = false,
@@ -98,8 +98,8 @@ object VcfFilter extends ToolCommand {
opt[Int]("minBamAlternateDepth") unbounded () valueName ("<int>") action { (x, c) =>
c.copy(minBamAlternateDepth = x)
} // TODO: Convert this to more generic filter
- opt[String]("denovoInSample") maxOccurs (1) unbounded () valueName ("<sample>") action { (x, c) =>
- c.copy(denovoInSample = x)
+ opt[String]("deNovoInSample") maxOccurs (1) unbounded () valueName ("<sample>") action { (x, c) =>
+ c.copy(deNovoInSample = x)
} text ("Only show variants that contain unique alleles in complete set for given sample")
opt[String]("mustHaveVariant") unbounded () valueName ("<sample>") action { (x, c) =>
c.copy(mustHaveVariant = x :: c.mustHaveVariant)
@@ -118,13 +118,13 @@ 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))
+ opt[Double]("minQualScore") unbounded () action { (x, c) =>
+ c.copy(minQualScore = Some(x))
} text ("Min qual score")
opt[String]("id") unbounded () action { (x, c) =>
c.copy(iDset = c.iDset + x)
} text ("Id that may pass the filter")
- opt[File]("id-file") unbounded () action { (x, c) =>
+ opt[File]("idFile") unbounded () action { (x, c) =>
c.copy(iDset = c.iDset ++ Source.fromFile(x).getLines())
} text ("File that contain list of IDs to get from vcf file")
}
@@ -183,8 +183,8 @@ object VcfFilter extends ToolCommand {
}
def minQualscore(record: VariantContext): Boolean = {
- if (commandArgs.minQualscore.isEmpty) return true
- record.getPhredScaledQual >= commandArgs.minQualscore.get
+ if (commandArgs.minQualScore.isEmpty) return true
+ record.getPhredScaledQual >= commandArgs.minQualScore.get
}
def filterRefCalls(record: VariantContext): Boolean = {
@@ -263,10 +263,10 @@ object VcfFilter extends ToolCommand {
}
def denovoInSample(record: VariantContext): Boolean = {
- if (commandArgs.denovoInSample == null) return true
- val genotype = record.getGenotype(commandArgs.denovoInSample)
+ if (commandArgs.deNovoInSample == null) return true
+ val genotype = record.getGenotype(commandArgs.deNovoInSample)
for (allele <- genotype.getAlleles if allele.isNonReference) {
- for (g <- record.getGenotypes if g.getSampleName != commandArgs.denovoInSample) {
+ for (g <- record.getGenotypes if g.getSampleName != commandArgs.deNovoInSample) {
if (g.getAlleles.exists(_.basesMatch(allele))) return false
}
}
--
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