From 4e6b4240be8e8df089fba43c4a01776535173746 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 29 Mar 2016 13:38:37 +0200
Subject: [PATCH] Added auto `sortInput` on retry
---
.../lumc/sasc/biopet/extensions/tools/GensToVcf.scala | 10 +++++++++-
.../scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala | 11 +++++------
2 files changed, 14 insertions(+), 7 deletions(-)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
index c620bc161..bab7b8fd5 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
@@ -45,6 +45,8 @@ class GensToVcf(val root: Configurable) extends ToolCommandFunction with Referen
var contig: String = _
+ var sortInput: Boolean = false
+
override def defaultCoreMemory = 5.0
override def beforeGraph(): Unit = {
@@ -54,13 +56,19 @@ class GensToVcf(val root: Configurable) extends ToolCommandFunction with Referen
if (outputVcf.getName.endsWith(".vcf.gz")) outputFiles :+= new File(outputVcf.getAbsolutePath + ".tbi")
}
+ override def setupRetry(): Unit = {
+ super.setupRetry()
+ sortInput = true
+ }
+
override def cmdLine = super.cmdLine +
required("--inputGenotypes", inputGens) +
required("--inputInfo", inputInfo) +
required("--outputVcf", outputVcf) +
optional("--contig", contig) +
required("--referenceFasta", reference) +
- required("--samplesFile", samplesFile)
+ required("--samplesFile", samplesFile) +
+ conditional(sortInput, "--sortInput")
}
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 143228366..e6f37c163 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
@@ -5,7 +5,7 @@ import java.util
import htsjdk.samtools.reference.{ FastaSequenceFile, ReferenceSequenceFileFactory }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
-import htsjdk.variant.variantcontext.{VariantContext, Allele, GenotypeBuilder, VariantContextBuilder}
+import htsjdk.variant.variantcontext.{ VariantContext, Allele, GenotypeBuilder, VariantContextBuilder }
import htsjdk.variant.vcf._
import nl.lumc.sasc.biopet.utils.ToolCommand
@@ -44,7 +44,7 @@ object GensToVcf extends ToolCommand {
opt[String]('c', "contig") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(contig = x)
} text "contig of impute file"
- opt[Unit]("sort") maxOccurs 1 action { (x, c) =>
+ opt[Unit]("sortInput") maxOccurs 1 action { (x, c) =>
c.copy(sortInput = true)
} text "In memory sorting"
}
@@ -86,13 +86,13 @@ object GensToVcf extends ToolCommand {
val lineIt: Iterator[Line] = {
val it = infoIt match {
case Some(x) => genotypeIt.zip(x).map(x => Line(x._1, Some(x._2)))
- case _ => genotypeIt.map(x => Line(x, None))
+ case _ => genotypeIt.map(x => Line(x, None))
}
if (cmdArgs.sortInput) {
logger.info("Start Sorting input files")
val list = it.toList
- val pos = list.map{ line =>
+ val pos = list.map { line =>
val values = line.genotype.split(" ")
val p = values(2).toInt
val alt = values(4)
@@ -100,8 +100,7 @@ object GensToVcf extends ToolCommand {
else p
}
list.zip(pos).sortBy(_._2).map(_._1).toIterator
- }
- else it
+ } else it
}
logger.info("Start processing genotypes")
--
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