From f58ba276d62000d4060577a8456ee4b53e38e9d8 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 10 Nov 2016 10:53:07 +0100
Subject: [PATCH] remove redundant imports, add scaladoc and autostyle fixes.
---
.../lumc/sasc/biopet/tools/VcfWithVcf.scala | 26 +++++++++++--------
.../sasc/biopet/tools/VcfWithVcfTest.scala | 4 +--
2 files changed, 17 insertions(+), 13 deletions(-)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
index 2eda5f4f0..ca6e077c7 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
@@ -17,10 +17,8 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.util
-import htsjdk.samtools.reference.FastaSequenceFile
import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
-import htsjdk.variant.vcf
import htsjdk.variant.vcf._
import nl.lumc.sasc.biopet.utils.{ FastaUtils, ToolCommand }
import nl.lumc.sasc.biopet.utils.VcfUtils.scalaListToJavaObjectArrayList
@@ -190,7 +188,6 @@ object VcfWithVcf extends ToolCommand {
}
}
-
def createRecord(fieldMap: Map[String, List[Any]], record: VariantContext,
fields: List[Fields], header: VCFHeader): VariantContext = {
fieldMap.foldLeft(new VariantContextBuilder(record))((builder, attribute) => {
@@ -216,18 +213,18 @@ object VcfWithVcf extends ToolCommand {
}
/**
- * Get the proper representation of a field from a secondary record given an original record
- * @param record original record
- * @param secondaryRecord secondary record
- * @param field field
- * @param header header of secondary record
- * @return
- */
+ * Get the proper representation of a field from a secondary record given an original record
+ * @param record original record
+ * @param secondaryRecord secondary record
+ * @param field field
+ * @param header header of secondary record
+ * @return
+ */
def getSecondaryField(record: VariantContext, secondaryRecord: VariantContext, field: String, header: VCFHeader): Any = {
header.getInfoHeaderLine(field).getCountType match {
case VCFHeaderLineCount.A => numberA(record, secondaryRecord, field)
case VCFHeaderLineCount.R => numberR(record, secondaryRecord, field)
- case _ => secondaryRecord.getAttribute(field)
+ case _ => secondaryRecord.getAttribute(field)
}
}
@@ -247,6 +244,13 @@ object VcfWithVcf extends ToolCommand {
toList
}
+ /**
+ * Get the correct values from a field that has number=R
+ * @param referenceRecord the reference record
+ * @param annotateRecord the to-be-annotated record
+ * @param field the field to annotate
+ * @return
+ */
def numberR(referenceRecord: VariantContext, annotateRecord: VariantContext, field: String): List[Any] = {
val refValues = referenceRecord.getAttributeAsList(field).toArray
annotateRecord.
diff --git a/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
index 287b7ad24..42039af4c 100644
--- a/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+++ b/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -236,9 +236,9 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
main(arguments)
val annotatedRecord = new VCFFileReader(tmpFile).iterator().next()
annotatedRecord.getAttribute("MULTI_ALL_ALLELE") match {
- case l: List[_] => l shouldBe List("C", "A")
+ case l: List[_] => l shouldBe List("C", "A")
case u: util.ArrayList[_] => u.toList shouldBe List("C", "A")
- case _ => throw new IllegalStateException("Not a list")
+ case _ => throw new IllegalStateException("Not a list")
}
}
--
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