From 4b6d158f7f83c0df76f0dc1fc89e5ef0d677029b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 24 Oct 2014 15:58:54 +0200
Subject: [PATCH] Added FastqSplitter to exe
---
.../sasc/biopet/core/BiopetExecutable.scala | 3 ++-
.../sasc/biopet/tools/FastqSplitter.scala | 27 +++++++++++++------
2 files changed, 21 insertions(+), 9 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
index d0134fd84..172e12d2b 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
@@ -28,7 +28,8 @@ object BiopetExecutable {
nl.lumc.sasc.biopet.tools.VcfFilter,
nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
nl.lumc.sasc.biopet.tools.BedToInterval,
- nl.lumc.sasc.biopet.tools.MpileupToVcf)
+ nl.lumc.sasc.biopet.tools.MpileupToVcf,
+ nl.lumc.sasc.biopet.tools.FastqSplitter)
)
/**
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
index 66cb83cc5..c59d8a246 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
@@ -4,6 +4,7 @@ import java.io.{ BufferedInputStream, File, FileInputStream, PrintWriter }
import java.util.zip.GZIPInputStream
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import scala.io.Source
+import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -19,24 +20,34 @@ class FastqSplitter(val root: Configurable) extends BiopetJavaCommandLineFunctio
override val defaultVmem = "8G"
memoryLimit = Option(4.0)
- override def commandLine = super.commandLine + required(input) + repeat(output)
+ override def commandLine = super.commandLine + required("-I", input) + repeat("-o", output)
}
-object FastqSplitter {
+object FastqSplitter extends ToolCommand {
+ case class Args (inputFile:File = null, outputFile:List[File] = Nil) extends AbstractArgs
+
+ class OptParser extends AbstractOptParser {
+ opt[File]('I', "inputFile") required() valueName("<file>") action { (x, c) =>
+ c.copy(inputFile = x) } text("out is a required file property")
+ opt[File]('o', "output") required() unbounded() valueName("<file>") action { (x, c) =>
+ c.copy(outputFile = x :: c.outputFile) } text("out is a required file property")
+ }
+
/**
* @param args the command line arguments
*/
def main(args: Array[String]): Unit = {
+ val argsParser = new OptParser
+ val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
val groupsize = 100
- val input = new File(args.head)
- val output: Array[PrintWriter] = new Array[PrintWriter](args.tail.size)
- for (t <- 1 to args.tail.size) output(t - 1) = new PrintWriter(args(t))
+ val output = for (file <- commandArgs.outputFile) yield new PrintWriter(file)
val inputStream = {
- if (input.getName.endsWith(".gz") || input.getName.endsWith(".gzip")) Source.fromInputStream(
+ if (commandArgs.inputFile.getName.endsWith(".gz") || commandArgs.inputFile.getName.endsWith(".gzip")) Source.fromInputStream(
new GZIPInputStream(
new BufferedInputStream(
- new FileInputStream(input)))).bufferedReader
- else Source.fromFile(input).bufferedReader
+ new FileInputStream(commandArgs.inputFile)))).bufferedReader
+ else Source.fromFile(commandArgs.inputFile).bufferedReader
}
while (inputStream.ready) {
for (writter <- output) {
--
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