From d55c268446ca2d371cfc54a6cb56efc9fb2428ce Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 12 Aug 2015 17:15:17 +0200
Subject: [PATCH] Review refactor
---
.../nl/lumc/sasc/biopet/tools/VcfFilter.scala | 18 +++++++------
.../sasc/biopet/tools/VcfFilterTest.scala | 25 ++++++++++---------
2 files changed, 23 insertions(+), 20 deletions(-)
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 0ddfc864a..981203de4 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
@@ -72,7 +72,7 @@ object VcfFilter extends ToolCommand {
minSamplesPass: Int = 1,
mustHaveVariant: List[String] = Nil,
calledIn: List[String] = Nil,
- mustHaveGenotype: List[String] = Nil,
+ mustHaveGenotype: List[(String, GenotypeType)] = Nil,
deNovoInSample: String = null,
resToDom: List[Trio] = Nil,
trioCompound: List[Trio] = Nil,
@@ -128,9 +128,11 @@ object VcfFilter extends ToolCommand {
c.copy(calledIn = x :: c.calledIn)
} text "Must be called in this sample"
opt[String]("mustHaveGenotype") unbounded () valueName "<sample:genotype>" action { (x, c) =>
- c.copy(mustHaveGenotype = x :: c.mustHaveGenotype)
- } validate { x => if (x.split(":").length == 2 && Set("HET", "HOM_REF", "HOM_VAR", "MIXED", "NO_CALL", "UNAVAILABLE").contains(x.split(":")(1))) success else failure("--mustHaveGenotype should be in this format: sample:genotype")
- } text "Must have genotoype <genotype> for this sample. Genotype can be HET, HOM_REF, HOM_VAR, MIXED, NO_CALL and UNAVAILABLE"
+ c.copy(mustHaveGenotype = (x.split(":")(0), GenotypeType.valueOf(x.split(":")(1))) :: c.mustHaveGenotype)
+ } validate { x =>
+ if (x.split(":").length == 2 && GenotypeType.values().contains(x.split(":")(1))) success
+ else failure("--mustHaveGenotype should be in this format: sample:genotype")
+ } text "Must have genotoype <genotype> for this sample. Genotype can be " + GenotypeType.values().mkString(", ")
opt[String]("diffGenotype") unbounded () valueName "<sample:sample>" action { (x, c) =>
c.copy(diffGenotype = (x.split(":")(0), x.split(":")(1)) :: c.diffGenotype)
} validate { x => if (x.split(":").length == 2) success else failure("--notSameGenotype should be in this format: sample:sample")
@@ -188,7 +190,8 @@ object VcfFilter extends ToolCommand {
hasMinSampleDepth(record, cmdArgs.minSampleDepth, cmdArgs.minSamplesPass) &&
minAlternateDepth(record, cmdArgs.minAlternateDepth, cmdArgs.minSamplesPass) &&
(cmdArgs.mustHaveVariant.isEmpty || mustHaveVariant(record, cmdArgs.mustHaveVariant)) &&
- calledIn(record, cmdArgs.calledIn) && hasGenotype(record, cmdArgs.mustHaveGenotype) &&
+ calledIn(record, cmdArgs.calledIn) &&
+ hasGenotype(record, cmdArgs.mustHaveGenotype) &&
(cmdArgs.diffGenotype.isEmpty || cmdArgs.diffGenotype.forall(x => notSameGenotype(record, x._1, x._2))) &&
(
cmdArgs.filterHetVarToHomVar.isEmpty ||
@@ -231,9 +234,8 @@ object VcfFilter extends ToolCommand {
* @param samplesGenotypes samples and their associated genotypes to be checked (of format sample:genotype)
* @return false when filter fails
*/
- def hasGenotype(record: VariantContext, samplesGenotypes: List[String]): Boolean = {
- if (!samplesGenotypes.forall(x => record.getGenotype(x.split(":")(0)).getType == GenotypeType.valueOf(x.split(":")(1)))) false
- else true
+ def hasGenotype(record: VariantContext, samplesGenotypes: List[(String, GenotypeType)]): Boolean = {
+ samplesGenotypes.forall(x => record.getGenotype(x._1).getType == x._2)
}
/**
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
index 2f4709a9c..2b47405a4 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.Paths
+import htsjdk.variant.variantcontext.GenotypeType
import htsjdk.variant.vcf.VCFFileReader
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
@@ -64,20 +65,20 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
- hasGenotype(record, List("Child_7006504:HET")) shouldBe true
- hasGenotype(record, List("Child_7006504:HOM_VAR")) shouldBe false
- hasGenotype(record, List("Child_7006504:HOM_REF")) shouldBe false
- hasGenotype(record, List("Child_7006504:NO_CALL")) shouldBe false
- hasGenotype(record, List("Child_7006504:MIXED")) shouldBe false
+ hasGenotype(record, List(("Child_7006504", GenotypeType.HET))) shouldBe true
+ hasGenotype(record, List(("Child_7006504", GenotypeType.HOM_VAR))) shouldBe false
+ hasGenotype(record, List(("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
+ hasGenotype(record, List(("Child_7006504", GenotypeType.NO_CALL))) shouldBe false
+ hasGenotype(record, List(("Child_7006504", GenotypeType.MIXED))) shouldBe false
- hasGenotype(record, List("Mother_7006508:HET")) shouldBe false
- hasGenotype(record, List("Mother_7006508:HOM_VAR")) shouldBe false
- hasGenotype(record, List("Mother_7006508:HOM_REF")) shouldBe true
- hasGenotype(record, List("Mother_7006508:NO_CALL")) shouldBe false
- hasGenotype(record, List("Mother_7006508:MIXED")) shouldBe false
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HET))) shouldBe false
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_VAR))) shouldBe false
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_REF))) shouldBe true
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.NO_CALL))) shouldBe false
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.MIXED))) shouldBe false
- hasGenotype(record, List("Mother_7006508:HOM_REF", "Child_7006504:HET")) shouldBe true
- hasGenotype(record, List("Mother_7006508:HET", "Child_7006504:HOM_HET")) shouldBe false
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_REF), ("Child_7006504", GenotypeType.HET))) shouldBe true
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HET), ("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
}
}
--
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