Commit 9a034f28 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 138ab51a
......@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.{Logging, VcfUtils, tryToParseNumber}
import nl.lumc.sasc.biopet.utils.{ Logging, VcfUtils, tryToParseNumber }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.io.Source
......@@ -285,7 +285,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
else {
(v1, v2) match {
case (x1: Int, x2: Int) => x1 + x2
case _ => throw new IllegalStateException(s"Value are not Int's, unable to sum them up, key: $key, v1: $v1, v2: $v2")
case _ => throw new IllegalStateException(s"Value are not Int's, unable to sum them up, key: $key, v1: $v1, v2: $v2")
}
}
}
......
......@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.{BiopetJavaCommandLineFunction, Reference}
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction with Reference {
analysisName = "CatVariants"
......
......@@ -24,7 +24,6 @@ import htsjdk.variant.vcf._
import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.JavaConversions._
import scala.collection.mutable.{ Map => MMap }
/**
* This tool parses a VEP annotated VCF into a standard VCF file.
......@@ -59,7 +58,7 @@ object VepNormalizer extends ToolCommand {
val header = reader.getFileHeader
val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().
setOutputFile(output).setReferenceDictionary(header.getSequenceDictionary)
build())
build ())
if (reader.iterator().hasNext) {
logger.debug("Checking for CSQ tag")
......@@ -97,8 +96,8 @@ object VepNormalizer extends ToolCommand {
/**
* Normalizer
*
* @param reader input VCF VCFFileReader
*
* @param reader input VCF VCFFileReader
* @param writer output VCF AsyncVariantContextWriter
* @param newInfos array of string containing names of new info fields
* @param mode normalizer mode (explode or standard)
......@@ -125,8 +124,8 @@ object VepNormalizer extends ToolCommand {
/**
* Checks whether header has a CSQ tag
*
* @param header VCF header
*
* @param header VCF header
*/
def csqCheck(header: VCFHeader) = {
if (!header.hasInfoLine("CSQ")) {
......@@ -139,8 +138,8 @@ object VepNormalizer extends ToolCommand {
* Checks whether version of input VCF is at least 4.0
* VEP is known to cause issues below 4.0
* Throws exception if not
*
* @param header VCFHeader of input VCF
*
* @param header VCFHeader of input VCF
*/
def versionCheck(header: VCFHeader) = {
var format = ""
......@@ -158,8 +157,8 @@ object VepNormalizer extends ToolCommand {
/**
* Parses the CSQ tag in the header
*
* @param header the VCF header
*
* @param header the VCF header
* @return list of strings with new info fields
*/
def parseCsq(header: VCFHeader): Array[String] = {
......@@ -170,8 +169,8 @@ object VepNormalizer extends ToolCommand {
/**
* Explode a single VEP-annotated record to multiple normal records
* Based on the number of annotated transcripts in the CSQ tag
*
* @param record the record as a VariantContext object
*
* @param record the record as a VariantContext object
* @param csqInfos An array with names of new info tags
* @return An array with the new records
*/
......
......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.utils
import java.io.File
import htsjdk.samtools.{SAMSequenceDictionary, SamReader, SamReaderFactory}
import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
import htsjdk.samtools.{ SAMSequenceDictionary, SamReader, SamReaderFactory }
import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
import scala.collection.JavaConversions._
import scala.collection.mutable
......@@ -146,12 +146,12 @@ object BamUtils {
/** This class will add functionality to [[SAMSequenceDictionary]] */
implicit class SamDictCheck(samDics: SAMSequenceDictionary) {
/**
* This method will check if all contig and sizes are the same without looking at the order of the contigs
*
* @throws AssertionError
* @param that Dict to compare to
* @param ignoreOrder When true the order of the contig does not matter
*/
* This method will check if all contig and sizes are the same without looking at the order of the contigs
*
* @throws AssertionError
* @param that Dict to compare to
* @param ignoreOrder When true the order of the contig does not matter
*/
def assertSameDictionary(that: SAMSequenceDictionary, ignoreOrder: Boolean): Unit = {
if (ignoreOrder) {
assert(samDics.getReferenceLength == that.getReferenceLength)
......
......@@ -21,11 +21,11 @@ import htsjdk.samtools.reference.FastaSequenceFile
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
import nl.lumc.sasc.biopet.extensions.bedtools.{BedtoolsIntersect, BedtoolsMerge}
import nl.lumc.sasc.biopet.extensions.gatk.{CatVariants, SelectVariants}
import nl.lumc.sasc.biopet.extensions.manwe.{ManweAnnotateVcf, ManweSamplesImport}
import nl.lumc.sasc.biopet.extensions.tools.{GvcfToBed, VcfWithVcf, VepNormalizer}
import nl.lumc.sasc.biopet.extensions.{Bgzip, Ln, VariantEffectPredictor}
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsIntersect, BedtoolsMerge }
import nl.lumc.sasc.biopet.extensions.gatk.{ CatVariants, SelectVariants }
import nl.lumc.sasc.biopet.extensions.manwe.{ ManweAnnotateVcf, ManweSamplesImport }
import nl.lumc.sasc.biopet.extensions.tools.{ GvcfToBed, VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Ln, VariantEffectPredictor }
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
......@@ -47,9 +47,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
def outputVcf: File = (gonlVcfFile, exacVcfFile) match {
case (Some(_), Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.exac.vcf.gz")
case (Some(_), _) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
case (_, Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
case _ => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.vcf.gz")
case (Some(_), _) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
case (_, Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
case _ => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.vcf.gz")
}
lazy val minScatterGenomeSize: Long = config("min_scatter_genome_size", default = 75000000)
......
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