Commit c1f9f9e8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Sync with develop and fix build issues

parent b230161f
......@@ -18,7 +18,8 @@ package nl.lumc.sasc.biopet.core
import java.io.{ File, FileInputStream }
import java.security.MessageDigest
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
......@@ -110,7 +111,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
if (executableToCanonicalPath) executable = file.getCanonicalPath
else executable = file.getAbsolutePath
} else {
BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
Logging.addError("executable: '" + executable + "' not found, please check config")
}
BiopetCommandLineFunction.executableCache += oldExecutable -> executable
BiopetCommandLineFunction.executableCache += executable -> executable
......
......@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* This class can pipe multiple BiopetCommandFunctions to 1 job
......
......@@ -55,7 +55,7 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with
reference = referenceFasta()
}
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
optional("--inputVcf", inputVcf) +
optional("--bamFile", bamFile) +
optional("--outputVariants", outputVariants) +
......
......@@ -38,7 +38,7 @@ class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 1.0
override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
override def cmdLine = super.cmdLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
}
object BedToInterval {
......
......@@ -32,7 +32,7 @@ class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntio
override def defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output)
}
......@@ -37,7 +37,7 @@ class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Sum
override def defaultCoreMemory = 6.0
override def commandLine = super.commandLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
override def cmdLine = super.cmdLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
def summaryFiles: Map[String, File] = Map()
......
......@@ -37,7 +37,7 @@ class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 4.0
/** * Generate command to execute */
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-I", input) +
repeat("-o", output)
}
......@@ -55,8 +55,8 @@ class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summariz
override def defaultCoreMemory = 4.0
// executed command line
override def commandLine =
super.commandLine +
override def cmdLine =
super.cmdLine +
required("-r", refFastq) +
required("-i", inputFastq1) +
required("-j", inputFastq2) +
......
......@@ -43,7 +43,7 @@ class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
}
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
repeat("-I", input) +
required("-o", output) +
required("-R", reference)
......
......@@ -65,8 +65,8 @@ class MergeTables(val root: Configurable) extends ToolCommandFuntion {
var delimiter: Option[String] = config("delimiter")
// executed command line
override def commandLine =
super.commandLine +
override def cmdLine =
super.cmdLine +
required("-i", idColumnIndices.mkString(",")) +
required("-a", valueColumnIndex) +
optional("-n", idColumnName) +
......
......@@ -66,14 +66,14 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
}
}
override def commandLine = {
override def cmdLine = {
(if (inputMpileup == null) {
val samtoolsMpileup = new SamtoolsMpileup(this)
samtoolsMpileup.reference = referenceFasta()
samtoolsMpileup.input = List(inputBam)
samtoolsMpileup.cmdPipe + " | "
} else "") +
super.commandLine +
super.cmdLine +
required("-o", output) +
optional("--minDP", minDP) +
optional("--minAP", minAP) +
......
......@@ -44,7 +44,7 @@ class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
* Creates command to execute extension
* @return
*/
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-i", inputFastq) +
required("-o", outputFastq) +
optional("-s", prefixSeq)
......
......@@ -32,7 +32,7 @@ class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output)
}
......@@ -44,7 +44,7 @@ class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-I", input) +
optional("--tag", tag) +
optional("--length", length) +
......
......@@ -44,7 +44,7 @@ class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-I", input) +
required("--tagLib", tagLib) +
optional("--countSense", countSense) +
......
......@@ -24,7 +24,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizab
override def defaultCoreMemory = 2.5
override def commandLine = super.commandLine + required("-i", input) + required("-o", output)
override def cmdLine = super.cmdLine + required("-i", input) + required("-o", output)
def summaryStats: Map[String, Any] = {
val map = ConfigUtils.fileToConfigMap(output)
......
......@@ -20,7 +20,7 @@ class SquishBed(val root: Configurable) extends ToolCommandFuntion {
var strandSensitive: Boolean = config("strandSensitive", default = false)
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output) +
conditional(strandSensitive, "-s")
......
......@@ -38,7 +38,7 @@ class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-I", inputVcf) +
required("-o", outputVcf) +
optional("--minSampleDepth", minSampleDepth) +
......
......@@ -69,7 +69,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summariza
}
/** Creates command to execute extension */
override def commandLine = super.commandLine +
override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", outputDir) +
repeat("--infoTag", infoTags) +
......
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