From 23f8d8aa8b49d9425221bda53d23c39846136ca2 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Fri, 14 Aug 2015 10:57:18 +0200
Subject: [PATCH] slight refactor for readability purposes
---
.../biopet/tools/BastyGenerateFasta.scala | 35 ++++++++++++++-----
1 file changed, 27 insertions(+), 8 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index 66f5ba800..deb9aa38c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
-import htsjdk.samtools.SamReaderFactory
+import htsjdk.samtools.{SAMSequenceRecord, SamReaderFactory}
import htsjdk.samtools.reference.IndexedFastaSequenceFile
import htsjdk.variant.variantcontext.VariantContext
import htsjdk.variant.vcf.VCFFileReader
@@ -28,6 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.mutable.ListBuffer
+import scala.collection.parallel.ParMap
class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
javaMainClass = getClass.getName
@@ -165,8 +166,12 @@ object BastyGenerateFasta extends ToolCommand {
val argsParser = new OptParser
cmdArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
- if (cmdArgs.outputVariants != null) writeVariantsOnly()
- if (cmdArgs.outputConsensus != null || cmdArgs.outputConsensusVariants != null) writeConsensus()
+ if (cmdArgs.outputVariants != null) {
+ writeVariantsOnly()
+ }
+ if (cmdArgs.outputConsensus != null || cmdArgs.outputConsensusVariants != null) {
+ writeConsensus()
+ }
}
protected def writeConsensus() {
@@ -271,14 +276,28 @@ object BastyGenerateFasta extends ToolCommand {
protected[tools] def getMaxAllele(vcfRecord: VariantContext)(implicit cmdArgs: Args): String = {
val maxSize = getLongestAllele(vcfRecord).getBases.length
- if (cmdArgs.sampleName == null) return fillAllele(vcfRecord.getReference.getBaseString, maxSize)
+ if (cmdArgs.sampleName == null) {
+ return fillAllele(vcfRecord.getReference.getBaseString, maxSize)
+ }
val genotype = vcfRecord.getGenotype(cmdArgs.sampleName)
- if (genotype == null) return fillAllele("", maxSize)
+
+ if (genotype == null) {
+ return fillAllele("", maxSize)
+ }
+
val AD = if (genotype.hasAD) genotype.getAD else Array.fill(vcfRecord.getAlleles.size())(cmdArgs.minAD)
- if (AD == null) return fillAllele("", maxSize)
+
+ if (AD == null) {
+ return fillAllele("", maxSize)
+ }
+
val maxADid = AD.zipWithIndex.maxBy(_._1)._2
- if (AD(maxADid) < cmdArgs.minAD) return fillAllele("", maxSize)
+
+ if (AD(maxADid) < cmdArgs.minAD) {
+ return fillAllele("", maxSize)
+ }
+
fillAllele(vcfRecord.getAlleles()(maxADid).getBaseString, maxSize)
}
-}
\ No newline at end of file
+}
--
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