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 af0d91dff9b5434d0f17c22193655a09007e215e..0b377b8800ae297bc5bcc3d9a14a7f4b5679e281 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
@@ -25,7 +25,10 @@ object BiopetExecutable {
nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
nl.lumc.sasc.biopet.tools.VcfToTsv,
nl.lumc.sasc.biopet.tools.VcfFilter,
- nl.lumc.sasc.biopet.tools.FindRepeatsPacBio)
+ nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
+ nl.lumc.sasc.biopet.tools.BedToInterval,
+ 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/BedToInterval.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
index 7b8e5003762f8c6d408b8a6f6fd31ec765958268..0a8cbdb3accf11ef641708b5a2dd4ac44f910467 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
@@ -4,6 +4,7 @@ import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMSequenceRecord
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.PrintWriter
@@ -27,7 +28,7 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
override def commandLine = super.commandLine + required(input) + required(bamFile) + required(output)
}
-object BedToInterval {
+object BedToInterval extends ToolCommand {
def apply(root: Configurable, inputBed: File, inputBam: File, outputDir: String): BedToInterval = {
val bedToInterval = new BedToInterval(root)
bedToInterval.input = inputBed
@@ -44,13 +45,25 @@ object BedToInterval {
return bedToInterval
}
+ case class Args (inputFile:File = null, outputFile:File = null) 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() valueName("<file>") action { (x, c) =>
+ c.copy(outputFile = x) } text("out is a required file property")
+ }
+
/**
* @param args the command line arguments
*/
def main(args: Array[String]): Unit = {
- val writer = new PrintWriter(args(2))
+ val argsParser = new OptParser
+ val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+ val writer = new PrintWriter(commandArgs.outputFile)
- val inputSam = new SAMFileReader(new File(args(1)))
+ val inputSam = new SAMFileReader(commandArgs.inputFile)
val refs = for (SQ <- inputSam.getFileHeader.getSequenceDictionary.getSequences.toArray) yield {
val record = SQ.asInstanceOf[SAMSequenceRecord]
writer.write("@SQ\tSN:" + record.getSequenceName + "\tLN:" + record.getSequenceLength + "\n")
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 66cb83cc5d32c3f597bcf9166a6714d96bbece93..c59d8a2464797f03eca4e0f7b2d6c3e0965ab624 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) {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index 8cc95f6733d351a25751dba309075a36248cb04a..a407a64de28c47de0a2c53033793a4b3c4f15a5e 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -50,46 +51,47 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
} else "") +
super.commandLine +
required("-o", output) +
- optional("-minDP", minDP) +
- optional("-minAP", minAP) +
- optional("-homoFraction", homoFraction) +
- optional("-ploidy", ploidy) +
- required("-sample", sample) +
+ optional("--minDP", minDP) +
+ optional("--minAP", minAP) +
+ optional("--homoFraction", homoFraction) +
+ optional("--ploidy", ploidy) +
+ required("--sample", sample) +
(if (inputBam == null) required("-I", inputMpileup) else "")
}
}
-object MpileupToVcf {
- var input: File = _
- var output: File = _
- var sample: String = _
- var minDP = 8
- var minAP = 2
- var homoFraction = 0.8
- var ploidy = 2
+object MpileupToVcf extends ToolCommand {
+ case class Args (input:File = null, output:File = null, sample:String = null, minDP:Int = 8, minAP:Int = 2,
+ homoFraction:Double = 0.8, ploidy:Int = 2) extends AbstractArgs
+
+ class OptParser extends AbstractOptParser {
+ opt[File]('I', "input") valueName("<file>") action { (x, c) =>
+ c.copy(input = x) } text("input, default is stdin")
+ opt[File]('o', "output") required() valueName("<file>") action { (x, c) =>
+ c.copy(output = x) } text("out is a required file property")
+ opt[String]('s', "sample") required() action { (x, c) =>
+ c.copy(sample = x) }
+ opt[Int]("minDP") required() action { (x, c) =>
+ c.copy(minDP = x) }
+ opt[Int]("minAP") required() action { (x, c) =>
+ c.copy(minAP = x) }
+ opt[Double]("homoFraction") required() action { (x, c) =>
+ c.copy(homoFraction = x) }
+ opt[Int]("ploidy") required() action { (x, c) =>
+ c.copy(ploidy = x) }
+ }
/**
* @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)
+
import scala.collection.mutable.Map
- for (t <- 0 until args.size) {
- args(t) match {
- case "-I" => input = new File(args(t+1))
- case "-o" => output = new File(args(t+1))
- case "-minDP" => minDP = args(t+1).toInt
- case "-minAP" => minAP = args(t+1).toInt
- case "-sample" => sample = args(t+1)
- case "-homoFraction" => homoFraction = args(t+1).toDouble
- case "-ploidy" => ploidy = args(t+1).toInt
- case _ =>
- }
- }
- if (input != null && !input.exists) throw new IllegalStateException("Input file does not exist")
- if (output == null) throw new IllegalStateException("Output file not found, use -o")
- if (sample == null) throw new IllegalStateException("sample not given, pls use -sample")
+ if (commandArgs.input != null && !commandArgs.input.exists) throw new IllegalStateException("Input file does not exist")
- val writer = new PrintWriter(output)
+ val writer = new PrintWriter(commandArgs.output)
writer.println("##fileformat=VCFv4.1")
writer.println("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">")
writer.println("##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">")
@@ -101,8 +103,8 @@ object MpileupToVcf {
writer.println("##FORMAT=<ID=AFC,Number=A,Type=Integer,Description=\"Alternetive Forward Reads\">")
writer.println("##FORMAT=<ID=ARC,Number=A,Type=Integer,Description=\"Alternetive Reverse Reads\">")
writer.println("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">")
- writer.println("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" + sample)
- val inputStream = if (input != null) Source.fromFile(input).getLines else Source.stdin.getLines
+ writer.println("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" + commandArgs.sample)
+ val inputStream = if (commandArgs.input != null) Source.fromFile(commandArgs.input).getLines else Source.stdin.getLines
class Counts(var forward:Int, var reverse:Int)
for (line <- inputStream;
val values = line.split("\t");
@@ -166,7 +168,7 @@ object MpileupToVcf {
format += ("RFC" -> counts(ref.toUpperCase).forward.toString)
format += ("RRC" -> counts(ref.toUpperCase).reverse.toString)
format += ("AD" -> (counts(ref.toUpperCase).forward + counts(ref.toUpperCase).reverse).toString)
- if (reads >= minDP) for ((key, value) <- counts if key != ref.toUpperCase if value.forward+value.reverse >= minAP) {
+ if (reads >= commandArgs.minDP) for ((key, value) <- counts if key != ref.toUpperCase if value.forward+value.reverse >= commandArgs.minAP) {
alt += key
format += ("AD" -> (format("AD") + "," + (value.forward + value.reverse).toString))
format += ("AFC" -> ( (if (format.contains("AFC")) format("AFC") + "," else "") + value.forward))
@@ -180,13 +182,13 @@ object MpileupToVcf {
var left = reads - dels
val gt = ArrayBuffer[Int]()
- for (p <- 0 to alt.size if gt.size < ploidy) {
+ for (p <- 0 to alt.size if gt.size < commandArgs.ploidy) {
var max = -1
for (a <- 0 until ad.length if ad(a) > (if (max >= 0) ad(max) else -1) && !gt.exists(_ == a)) max = a
val f = ad(max).toDouble / left
- for (a <- 0 to floor(f).toInt if gt.size < ploidy) gt.append(max)
- if (f - floor(f) >= homoFraction) {
- for (b <- p to ploidy if gt.size < ploidy) gt.append(max)
+ for (a <- 0 to floor(f).toInt if gt.size < commandArgs.ploidy) gt.append(max)
+ if (f - floor(f) >= commandArgs.homoFraction) {
+ for (b <- p to commandArgs.ploidy if gt.size < commandArgs.ploidy) gt.append(max)
}
left -= ad(max)
}