Skip to content

GitLab

Commit 385c71e9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Biopet core code inspection round

parent c181bccd
Hide whitespace changes
Inline Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @ 385c71e9
......@@ -44,7 +44,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
private[summary] var summaryQScripts: List[SummaryQScript] = Nil
/** Name of the pipeline in the summary */
var summaryName = configNamespace
var summaryName: String = configNamespace
/** Must return a map with used settings for this pipeline */
def summarySettings: Map[String, Any]
......@@ -98,7 +98,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
Await.result(
SummaryDb.openSqliteSummary(summaryDbFile).getRuns(runId = Some(id)).map(_.headOption),
Duration.Inf) match {
case Some(x) => id
case Some(_) => id
case _ =>
logger.warn(
s"Run id found in '$runIdFile' does not exist in summary, creating a new run")
......@@ -191,22 +191,22 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
qscript match {
case q: MultiSampleQScript =>
// Global level
for ((key, file) <- qscript.summaryFiles) addChecksum(file)
for ((_, file) <- qscript.summaryFiles) addChecksum(file)
for ((sampleName, sample) <- q.samples) {
for ((_, sample) <- q.samples) {
// Sample level
for ((key, file) <- sample.summaryFiles) addChecksum(file)
for ((libName, lib) <- sample.libraries) {
for ((_, file) <- sample.summaryFiles) addChecksum(file)
for ((_, lib) <- sample.libraries) {
// Library level
for ((key, file) <- lib.summaryFiles) addChecksum(file)
for ((_, file) <- lib.summaryFiles) addChecksum(file)
}
}
case q => for ((key, file) <- q.summaryFiles) addChecksum(file)
case q => for ((_, file) <- q.summaryFiles) addChecksum(file)
}
for (inputFile <- inputFiles) {
inputFile.md5 match {
case Some(checksum) => {
case Some(checksum) =>
val checkMd5 = new CheckChecksum
checkMd5.inputFile = inputFile.file
if (!SummaryQScript.md5sumCache.contains(inputFile.file))
......@@ -216,7 +216,6 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
checkMd5.jobOutputFile = new File(checkMd5.checksumFile.getParentFile,
checkMd5.checksumFile.getName + ".check.out")
add(checkMd5)
}
case _ =>
}
}
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @ 385c71e9
......@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.Input
import scala.collection.mutable
import scala.io.Source
import scala.concurrent.Await
import scala.concurrent.{Await, Future}
import scala.concurrent.duration.Duration
import scala.concurrent.ExecutionContext.Implicits.global
......@@ -40,7 +40,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
require(parent != null)
/** To access qscript for this summary */
val qscript = parent
val qscript: SummaryQScript = parent
@Input(doc = "deps", required = false)
var deps: List[File] = Nil
......@@ -62,28 +62,27 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
if (qscript == root) { // This initialize the database
qscript match {
case s: MultiSampleQScript => s.initSummaryDb
case s: MultiSampleQScript => s.initSummaryDb()
case t: SampleLibraryTag =>
t.sampleId.foreach {
case sampleName =>
sampleName =>
val sampleId = Await
.result(db.getSamples(name = Some(sampleName), runId = Some(qscript.summaryRunId))
.map(_.headOption.map(_.id)),
Duration.Inf)
.map(_.headOption.map(_.id)),
Duration.Inf)
.getOrElse {
Await.result(db.createOrUpdateSample(sampleName, qscript.summaryRunId),
Duration.Inf)
Duration.Inf)
}
t.libId.foreach { libName =>
val libId = Await
.result(db.getSamples(name = Some(libName),
runId = Some(qscript.summaryRunId),
sampleId = Some(sampleId))
.map(_.headOption.map(_.id)),
Duration.Inf)
Await.result(db.getSamples(name = Some(libName),
runId = Some(qscript.summaryRunId),
sampleId = Some(sampleId))
.map(_.headOption.map(_.id)),
Duration.Inf)
.getOrElse {
Await.result(db.createOrUpdateLibrary(libName, qscript.summaryRunId, sampleId),
Duration.Inf)
Duration.Inf)
}
}
}
......@@ -102,7 +101,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
try {
deps :+= f.firstOutput
} catch {
case e: NullPointerException => logger.debug("Queue values are not initialized")
case _: NullPointerException => logger.debug("Queue values are not initialized")
}
case _ =>
}
......@@ -328,7 +327,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
}
/** Convert summarizable to a summary map */
def parseSummarizable(summarizable: Summarizable, name: String) = {
def parseSummarizable(summarizable: Summarizable, name: String): Map[String, Any] = {
val stats = summarizable.summaryStats
val files = parseFiles(summarizable.summaryFiles)
......@@ -365,11 +364,11 @@ object WriteSummary {
libId: Option[Int],
key: String,
file: File,
outputDir: File) = {
outputDir: File): Future[Int] = {
val path = if (file.getAbsolutePath.startsWith(outputDir.getAbsolutePath + File.separator)) {
"." + file.getAbsolutePath.stripPrefix(s"${outputDir.getAbsolutePath}")
} else file.getAbsolutePath
val md5 = SummaryQScript.md5sumCache.get(file).map(WriteSummary.parseChecksum(_))
val md5 = SummaryQScript.md5sumCache.get(file).map(WriteSummary.parseChecksum)
val size = if (file.exists()) file.length() else 0L
val link = if (file.exists()) java.nio.file.Files.isSymbolicLink(file.toPath) else false
db.createOrUpdateFile(runId,
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
View file @ 385c71e9
......@@ -98,7 +98,7 @@ object BiopetQCommandLine extends GatkLogging {
System.exit(CommandLineProgram.result)
}
val timestamp = System.currentTimeMillis
val timestamp: Long = System.currentTimeMillis
}
/**
......@@ -135,7 +135,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
// override createByType to pass the correct exceptions
new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL)) {
override def createByType(plugintype: Class[_ <: QScript]) = {
override def createByType(plugintype: Class[_ <: QScript]): QScript = {
val noArgsConstructor = plugintype.getDeclaredConstructor()
noArgsConstructor.setAccessible(true)
noArgsConstructor.newInstance()
......@@ -157,7 +157,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
* Takes the QScripts passed in, runs their script() methods, retrieves their generated
* functions, and then builds and runs a QGraph based on the dependencies.
*/
def execute = {
def execute: Int = {
var success = false
var result = 1
var functionsAndStatusSize = 0
......@@ -181,7 +181,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
}
qGraph.messengers =
allCommandPlugins.filter(_.statusMessenger != null).map(_.statusMessenger).toSeq
allCommandPlugins.filter(_.statusMessenger != null).map(_.statusMessenger)
// TODO: Default command plugin argument?
val remoteFileConverter =
......@@ -270,7 +270,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
* so that their arguments can be inspected before QScript.script is called.
* @return Array of dynamic sources
*/
override def getArgumentSources = {
override def getArgumentSources: Array[Class[_]] = {
var plugins = Seq.empty[Class[_]]
plugins ++= qScriptPluginManager.getPlugins
plugins ++= qCommandPlugin.getPlugins
......@@ -281,7 +281,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
* Returns the name of a script/plugin
* @return The name of a script/plugin
*/
override def getArgumentSourceName(source: Class[_]) = {
override def getArgumentSourceName(source: Class[_]): String = {
if (classOf[QScript].isAssignableFrom(source))
qScriptPluginManager.getName(source.asSubclass(classOf[QScript]))
else if (classOf[QCommandPlugin].isAssignableFrom(source))
......@@ -294,7 +294,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
* Returns a ScalaCompoundArgumentTypeDescriptor that can parse argument sources into scala collections.
* @return a ScalaCompoundArgumentTypeDescriptor
*/
override def getArgumentTypeDescriptors =
override def getArgumentTypeDescriptors: util.List[ArgumentTypeDescriptor] =
util.Arrays.asList(new ScalaCompoundArgumentTypeDescriptor)
override def getApplicationDetails: ApplicationDetails = {
......@@ -338,7 +338,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
}
}
def shutdown() = {
def shutdown(): AnyVal = {
shuttingDown = true
qGraph.shutdown()
if (qScriptClasses != null) IOUtils.tryDelete(qScriptClasses)
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
View file @ 385c71e9
......@@ -39,8 +39,8 @@ class BamStats(val parent: Configurable)
var outputDir: File = _
var binSize: Option[Int] = config("bin_size")
var threadBinSize: Option[Int] = config("thread_bin_size")
val binSize: Option[Int] = config("bin_size")
val threadBinSize: Option[Int] = config("thread_bin_size")
override def defaultThreads = 3
override def defaultCoreMemory = 5.0
......@@ -68,7 +68,7 @@ class BamStats(val parent: Configurable)
}
/** Creates command to execute extension */
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-b", bamFile) +
required("-o", outputDir) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
View file @ 385c71e9
......@@ -43,8 +43,8 @@ class BastyGenerateFasta(val parent: Configurable) extends ToolCommandFunction w
var snpsOnly: Boolean = config("snps_only", default = false)
var sampleName: String = _
var minAD: Int = config("min_ad", default = 8)
var minDepth: Int = config("min_depth", default = 8)
val minAD: Int = config("min_ad", default = 8)
val minDepth: Int = config("min_depth", default = 8)
var outputName: String = _
override def defaultCoreMemory = 4.0
......@@ -54,7 +54,7 @@ class BastyGenerateFasta(val parent: Configurable) extends ToolCommandFunction w
reference = referenceFasta()
}
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
optional("--inputVcf", inputVcf) +
optional("--bamFile", bamFile) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
View file @ 385c71e9
......@@ -37,7 +37,7 @@ class BedToInterval(val parent: Configurable) extends ToolCommandFunction {
override def defaultCoreMemory = 1.0
override def cmdLine =
override def cmdLine: String =
super.cmdLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
}
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
View file @ 385c71e9
......@@ -31,7 +31,7 @@ class BedtoolsCoverageToCounts(val parent: Configurable) extends ToolCommandFunc
override def defaultCoreMemory = 3.0
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-I", input) +
required("-o", output)
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
View file @ 385c71e9
......@@ -37,7 +37,7 @@ class BiopetFlagstat(val parent: Configurable) extends ToolCommandFunction with
override def defaultCoreMemory = 6.0
override def cmdLine =
override def cmdLine: String =
super.cmdLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
def summaryFiles: Map[String, File] = Map()
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/CheckValidateAnnotation.scala
View file @ 385c71e9
......@@ -40,7 +40,7 @@ class CheckValidateAnnotation(val parent: Configurable)
var genomeName: String = ""
/** Exits whenever the input md5sum is not the same as the output md5sum */
def run: Unit = {
def run(): Unit = {
val reader = Source.fromFile(inputLogFile)
reader.getLines().foreach { line =>
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala
View file @ 385c71e9
......@@ -29,7 +29,7 @@ class DownloadNcbiAssembly(val parent: Configurable) extends ToolCommandFunction
var outputReport: File = _
@Input(required = true)
var assemblyReport: File = null
var assemblyReport: File = _
var nameHeader: Option[String] = None
......@@ -38,7 +38,7 @@ class DownloadNcbiAssembly(val parent: Configurable) extends ToolCommandFunction
override def defaultCoreMemory = 4.0
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-a", assemblyReport) +
required("--report", outputReport) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
View file @ 385c71e9
......@@ -36,7 +36,7 @@ class FastqSplitter(val parent: Configurable) extends ToolCommandFunction {
override def defaultCoreMemory = 4.0
/** * Generate command to execute */
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-I", input) +
repeat("-o", output)
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
View file @ 385c71e9
......@@ -35,31 +35,31 @@ class FastqSync(val parent: Configurable) extends ToolCommandFunction with Summa
/** Original FASTQ file (read 1 or 2) */
@Input(required = true)
var refFastq: File = null
var refFastq: File = _
/** "Input read 1 FASTQ file" */
@Input(required = true)
var inputFastq1: File = null
var inputFastq1: File = _
/** Input read 2 FASTQ file */
@Input(required = true)
var inputFastq2: File = null
var inputFastq2: File = _
/** Output read 1 FASTQ file */
@Output(required = true)
var outputFastq1: File = null
var outputFastq1: File = _
/** Output read 2 FASTQ file */
@Output(required = true)
var outputFastq2: File = null
var outputFastq2: File = _
/** Sync statistics */
@Output(required = true)
var outputStats: File = null
var outputStats: File = _
override def defaultCoreMemory = 4.0
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-r", refFastq) +
required("-i", inputFastq1) +
......@@ -98,7 +98,7 @@ class FastqSync(val parent: Configurable) extends ToolCommandFunction with Summa
"num_reads_kept" -> countRLeft)
}
override def summaryDeps = outputStats :: super.summaryDeps
override def summaryDeps: List[File] = outputStats :: super.summaryDeps
override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
(v1, v2) match {
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
View file @ 385c71e9
......@@ -63,7 +63,7 @@ class GensToVcf(val parent: Configurable) extends ToolCommandFunction with Refer
sortInput = true
}
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("--inputGenotypes", inputGens) +
required("--inputInfo", inputInfo) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala
View file @ 385c71e9
......@@ -32,18 +32,13 @@ class GvcfToBed(val parent: Configurable) extends ToolCommandFunction {
@Output(doc = "output bed")
var outputBed: File = _
@Argument(doc = "sample", required = false)
var sample: Option[String] = None
@Argument(doc = "minquality", required = false)
var minQuality: Int = 0
@Argument(doc = "inverse", required = false)
var inverse: Option[File] = None
override def defaultCoreMemory = 4.0
override def cmdLine = {
override def cmdLine: String = {
super.cmdLine +
required("-I", inputVcf) +
required("-O", outputBed) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
View file @ 385c71e9
......@@ -44,7 +44,7 @@ class KrakenReportToJson(val parent: Configurable) extends ToolCommandFunction w
override def defaultCoreMemory = 4.0
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-i", inputReport) +
required("-o", output) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
View file @ 385c71e9
......@@ -16,11 +16,11 @@ package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommandFunction
import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
class MergeAlleles(val parent: Configurable) extends ToolCommandFunction {
class MergeAlleles(val parent: Configurable) extends ToolCommandFunction with Reference {
def toolObject = nl.lumc.sasc.biopet.tools.MergeAlleles
@Input(doc = "Input vcf files", shortName = "input", required = true)
......@@ -32,17 +32,18 @@ class MergeAlleles(val parent: Configurable) extends ToolCommandFunction {
@Output(doc = "Output vcf file index", shortName = "output", required = true)
private var outputIndex: File = _
var reference: File = config("reference")
var reference: File = _
override def defaultCoreMemory = 1.0
override def beforeGraph() {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
}
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
repeat("-I", input) +
required("-o", output) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala
View file @ 385c71e9
......@@ -31,11 +31,11 @@ class MergeOtuMaps(val parent: Configurable) extends ToolCommandFunction {
@Output(doc = "Output", shortName = "output", required = true)
var output: File = _
var skipPrefix: List[String] = config("skip_prefix", default = Nil)
val skipPrefix: List[String] = config("skip_prefix", default = Nil)
override def defaultCoreMemory = 6.0
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
repeat("-I", input) +
required("-o", output) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
View file @ 385c71e9
......@@ -39,7 +39,7 @@ class MergeTables(val parent: Configurable) extends ToolCommandFunction {
/** Output file */
@Output(doc = "Output merged table", required = true)
var output: File = null
var output: File = _
// TODO: should be List[Int] really
/** List of column indices to combine to make a unique identifier per row */
......@@ -49,7 +49,7 @@ class MergeTables(val parent: Configurable) extends ToolCommandFunction {
var valueColumnIndex: Int = config("value_column_index", default = 2)
/** Name of the identifier column in the output file */
var idColumnName: Option[String] = config("id_column_name")
val idColumnName: Option[String] = config("id_column_name")
/** Common file extension of all input files */
var fileExtension: Option[String] = config("file_extension")
......@@ -61,10 +61,10 @@ class MergeTables(val parent: Configurable) extends ToolCommandFunction {
var fallbackString: Option[String] = config("fallback_string")
/** Column delimiter of each input file (used for splitting into columns */
var delimiter: Option[String] = config("delimiter")
val delimiter: Option[String] = config("delimiter")
// executed command line
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-i", idColumnIndices.mkString(",")) +
required("-a", valueColumnIndex) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
View file @ 385c71e9
......@@ -64,7 +64,7 @@ class MpileupToVcf(val parent: Configurable) extends ToolCommandFunction with Re
}
}
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-o", output) +
optional("--minDP", minDP) +
......
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/NcbiReportToContigMap.scala
View file @ 385c71e9
......@@ -35,7 +35,7 @@ class NcbiReportToContigMap(val parent: Configurable) extends ToolCommandFunctio
override def defaultCoreMemory = 4.0
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-a", assemblyReport) +
required("--report", outputReport) +
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment