From 48f983ae9dd55f58037b71d9598122445e74c204 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 25 Mar 2016 14:27:35 +0100
Subject: [PATCH] Fix style warnings
---
.../scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
index a35157570..35fbc747d 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
@@ -3,14 +3,13 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.util
-import htsjdk.samtools.reference.{ReferenceSequenceFileFactory, ReferenceSequenceFileWalker, ReferenceSequenceFile, FastaSequenceFile}
+import htsjdk.samtools.reference.{ FastaSequenceFile, ReferenceSequenceFileFactory }
+import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.variantcontext.{ Allele, GenotypeBuilder, VariantContextBuilder }
-import htsjdk.variant.variantcontext.writer.{ VariantContextWriterBuilder, AsyncVariantContextWriter }
import htsjdk.variant.vcf._
import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.JavaConversions._
-
import scala.io.Source
/**
@@ -81,15 +80,13 @@ object GensToVcf extends ToolCommand {
val start = genotypeValues(2).toInt
if (genotypeValues(4) == "-") {
val seq = fastaFile.getSubsequenceAt(cmdArgs.contig, start - 1, start + genotypeValues(4).length - 1)
- (start - 1, (start + genotypeValues(4).length - 1),
+ (start - 1, start + genotypeValues(4).length - 1,
Allele.create(new String(seq.getBases), true), Allele.create(new String(Array(seq.getBases.head))))
} else {
val ref = Allele.create(genotypeValues(3), true)
- (start, (ref.length - 1 + start), Allele.create(genotypeValues(3), true), Allele.create(genotypeValues(4)))
+ (start, ref.length - 1 + start, Allele.create(genotypeValues(3), true), Allele.create(genotypeValues(4)))
}
}
- //val start = genotypeValues(2).toInt
- //val end = ref.length - 1 + start
val genotypes = samples.toList.zipWithIndex.map {
case (sampleName, index) =>
val gps = Array(
--
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