From 7f2580f2a7f00094e2f3af6c958bc422618d408b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 1 Jul 2015 19:11:23 +0200
Subject: [PATCH] Fixing code warning from ide
---
.../core/BiopetCommandLineFunction.scala | 4 +-
.../core/BiopetCommandLineFunctionTrait.scala | 44 +++++++++----------
.../sasc/biopet/core/BiopetExecutable.scala | 26 +++++------
.../core/BiopetJavaCommandLineFunction.scala | 6 +--
.../lumc/sasc/biopet/core/BiopetQScript.scala | 38 +++++++---------
.../sasc/biopet/core/MultiSampleQScript.scala | 15 +++----
.../sasc/biopet/core/PipelineCommand.scala | 10 ++---
.../nl/lumc/sasc/biopet/core/Reference.scala | 11 ++++-
.../lumc/sasc/biopet/core/ToolCommand.scala | 12 +++--
.../biopet/core/summary/Summarizable.scala | 4 +-
.../sasc/biopet/core/summary/Summary.scala | 4 +-
.../biopet/core/summary/SummaryQScript.scala | 20 ++++-----
.../biopet/core/summary/SummaryValue.scala | 7 +--
.../lumc/sasc/biopet/extensions/Fastqc.scala | 4 +-
.../extensions/conifer/ConiferExport.scala | 4 +-
.../biopet/pipelines/shiva/ShivaReport.scala | 22 +++++-----
16 files changed, 112 insertions(+), 119 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index b73f76c7b..30c400bc5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -31,9 +31,9 @@ abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait
* @return Command to run
*/
final def commandLine: String = {
- preCmdInternal
+ preCmdInternal()
val cmd = cmdLine
addJobReportBinding("command", cmd)
- return cmd
+ cmd
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index e732abbfa..a946349c3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.queue.QException
import org.broadinstitute.gatk.queue.function.CommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+import org.broadinstitute.gatk.utils.commandline.Input
+import scala.collection.mutable
import scala.sys.process.{ Process, ProcessLogger }
import scala.util.matching.Regex
import java.io.FileInputStream
@@ -50,15 +50,15 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
* Can override this method. This is executed just before the job is ready to run.
* Can check on run time files from pipeline here
*/
- protected[core] def beforeCmd {}
+ protected[core] def beforeCmd() {}
/** Can override this method. This is executed after the script is done en queue starts to generate the graph */
- protected[core] def beforeGraph {}
+ protected[core] def beforeGraph() {}
/** Set default output file, threads and vmem for current job */
override def freezeFieldValues() {
- preProcesExecutable
- beforeGraph
+ preProcessExecutable()
+ beforeGraph()
if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
if (threads == 0) threads = getThreads(defaultThreads)
@@ -95,7 +95,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/**
* Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
*/
- protected[core] def preProcesExecutable {
+ protected[core] def preProcessExecutable() {
if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
try if (executable != null) {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
@@ -135,10 +135,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
/** executes checkExecutable method and fill job report */
- final protected def preCmdInternal {
- preProcesExecutable
-
- beforeCmd
+ final protected def preCmdInternal() {
+ preProcessExecutable()
+ beforeCmd()
addJobReportBinding("cores", nCoresRequest match {
case Some(n) if n > 0 => n
@@ -157,7 +156,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
protected val versionExitcode = List(0)
/** Executes the version command */
- private[core] def getVersionInternal(): Option[String] = {
+ private[core] def getVersionInternal: Option[String] = {
if (versionCommand == null || versionRegex == null) None
else getVersionInternal(versionCommand, versionRegex)
}
@@ -173,7 +172,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
"\n output log: \n stdout: \n" + stdout.toString +
"\n stderr: \n" + stderr.toString
val process = Process(versionCommand).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
- if (!versionExitcode.contains(process.exitValue)) {
+ if (!versionExitcode.contains(process.exitValue())) {
logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
return None
}
@@ -184,13 +183,13 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
}
logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
- return None
+ None
}
/** Get version from cache otherwise execute the version command */
def getVersion: Option[String] = {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
- preProcesExecutable
+ preProcessExecutable()
if (!BiopetCommandLineFunctionTrait.versionCache.contains(versionCommand))
getVersionInternal match {
case Some(version) => BiopetCommandLineFunctionTrait.versionCache += versionCommand -> version
@@ -207,8 +206,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
def getThreads(default: Int): Int = {
val maxThreads: Int = config("maxthreads", default = 8)
val threads: Int = config("threads", default = default)
- if (maxThreads > threads) return threads
- else return maxThreads
+ if (maxThreads > threads) threads
+ else maxThreads
}
/**
@@ -220,15 +219,14 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
def getThreads(default: Int, module: String): Int = {
val maxThreads: Int = config("maxthreads", default = 8, submodule = module)
val threads: Int = config("threads", default = default, submodule = module)
- if (maxThreads > threads) return threads
- else return maxThreads
+ if (maxThreads > threads) threads
+ else maxThreads
}
}
/** stores global caches */
object BiopetCommandLineFunctionTrait {
- import scala.collection.mutable.Map
- private[core] val versionCache: Map[String, String] = Map()
- private[core] val executableMd5Cache: Map[String, String] = Map()
- private[core] val executableCache: Map[String, String] = Map()
+ private[core] val versionCache: mutable.Map[String, String] = mutable.Map()
+ private[core] val executableMd5Cache: mutable.Map[String, String] = mutable.Map()
+ private[core] val executableCache: mutable.Map[String, String] = mutable.Map()
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
index c0febb8fe..83eb2da68 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
@@ -23,6 +23,9 @@ import org.apache.log4j.Logger
import nl.lumc.sasc.biopet.{ FullVersion, LastCommitHash }
import nl.lumc.sasc.biopet.core.BiopetExecutable._
+/**
+ * This is the main trait for the biopet executable
+ */
trait BiopetExecutable extends Logging {
def pipelines: List[MainCommand]
@@ -74,7 +77,7 @@ trait BiopetExecutable extends Logging {
def getCommand(module: String, name: String): MainCommand = {
checkModule(module)
val command = modules(module).find(p => p.commandName.toLowerCase == name.toLowerCase)
- if (command == None) {
+ if (command.isEmpty) {
System.err.println(s"ERROR: command '$name' does not exist in module '$module'\n" + usage(module))
System.exit(1)
}
@@ -82,22 +85,20 @@ trait BiopetExecutable extends Logging {
}
args match {
- case Array("version") => {
+ case Array("version") =>
println("version: " + FullVersion)
- }
- case Array("license") => {
+ case Array("license") =>
println(getLicense)
- }
- case Array(module, name, passArgs @ _*) => {
+ case Array(module, name, passArgs @ _*) =>
try {
getCommand(module, name).main(passArgs.toArray)
} catch {
- case e: Exception => {
+ case e: Exception =>
val sWriter = new StringWriter()
val pWriter = new PrintWriter(sWriter)
e.printStackTrace(pWriter)
pWriter.close()
- val trace = (sWriter.toString.split("\n"))
+ val trace = sWriter.toString.split("\n")
if (!logger.isDebugEnabled) {
trace.filterNot(_.startsWith("\tat")).foreach(logger.error(_))
@@ -106,20 +107,17 @@ trait BiopetExecutable extends Logging {
trace.foreach(logger.debug(_))
}
sys.exit(1)
- }
}
- }
- case Array(module) => {
+ case Array(module) =>
System.err.println(usage(module))
sys.exit(1)
- }
- case _ => {
+ case _ =>
System.err.println(usage())
sys.exit(1)
- }
}
}
+ /** This function checks if current build is based on a dirty repository (uncommitted changes) */
def checkDirtyBuild(logger: Logger): Unit =
if (LastCommitHash.endsWith("-dirty")) {
logger.warn("***********************************************************")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index 6904cdcd0..c659947d0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -33,17 +33,17 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
/** Creates command to execute extension */
override def commandLine: String = {
- preCmdInternal
+ preCmdInternal()
val cmd = super.commandLine
val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
- return cmd
+ cmd
}
def javaVersionCommand: String = executable + " -version"
def getJavaVersion: Option[String] = {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
- preProcesExecutable
+ preProcessExecutable()
if (!BiopetCommandLineFunctionTrait.versionCache.contains(javaVersionCommand))
getVersionInternal(javaVersionCommand, """java version "(.*)"""".r) match {
case Some(version) => BiopetCommandLineFunctionTrait.versionCache += javaVersionCommand -> version
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 6154e7660..c80ac4ac1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -16,14 +16,15 @@
package nl.lumc.sasc.biopet.core
import java.io.File
-import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.config.{ ConfigValueIndex, Config, Configurable }
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder }
-import org.broadinstitute.gatk.utils.commandline.Argument
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
-import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import org.broadinstitute.gatk.queue.util.{Logging => GatkLogging}
+import org.broadinstitute.gatk.utils.commandline.Argument
+
import scala.collection.mutable.ListBuffer
/** Base for biopet pipeline */
@@ -53,10 +54,10 @@ trait BiopetQScript extends Configurable with GatkLogging {
var functions: Seq[QFunction]
/** Init for pipeline */
- def init
+ def init()
/** Pipeline itself */
- def biopetScript
+ def biopetScript()
/** Returns the extension to make the report */
def reportClass: Option[ReportBuilderExtension] = None
@@ -65,19 +66,18 @@ trait BiopetQScript extends Configurable with GatkLogging {
final def script() {
outputDir = config("output_dir")
outputDir = outputDir.getAbsoluteFile
- init
- biopetScript
+ init()
+ biopetScript()
if (disableScatter) for (function <- functions) function match {
case f: ScatterGatherableFunction => f.scatterCount = 1
case _ =>
}
for (function <- functions) function match {
- case f: BiopetCommandLineFunctionTrait => {
- f.preProcesExecutable
- f.beforeGraph
+ case f: BiopetCommandLineFunctionTrait =>
+ f.preProcessExecutable()
+ f.beforeGraph()
f.commandLine
- }
case _ =>
}
@@ -87,7 +87,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
reportClass.foreach(add(_))
- BiopetQScript.checkErrors
+ BiopetQScript.checkErrors()
}
/** Get implemented from org.broadinstitute.gatk.queue.QScript */
@@ -96,11 +96,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
/** Get implemented from org.broadinstitute.gatk.queue.QScript */
def addAll(functions: scala.Traversable[org.broadinstitute.gatk.queue.function.QFunction])
- /**
- * Function to set isIntermediate and add in 1 line
- * @param function
- * @param isIntermediate
- */
+ /** Function to set isIntermediate and add in 1 line */
def add(function: QFunction, isIntermediate: Boolean = false) {
function.isIntermediate = isIntermediate
add(function)
@@ -115,8 +111,8 @@ object BiopetQScript extends Logging {
errors.append(new Exception(msg))
}
- protected def checkErrors: Unit = {
- if (!errors.isEmpty) {
+ protected def checkErrors(): Unit = {
+ if (errors.nonEmpty) {
logger.error("*************************")
logger.error("Biopet found some errors:")
if (logger.isDebugEnabled) {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 837fc37a7..f7280dcb4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -17,10 +17,9 @@ package nl.lumc.sasc.biopet.core
import java.io.File
-import nl.lumc.sasc.biopet.core.config.{ Config }
import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.utils.commandline.{ Argument }
+import org.broadinstitute.gatk.utils.commandline.Argument
/** This trait creates a structured way of use multisample pipelines */
trait MultiSampleQScript extends SummaryQScript {
@@ -107,11 +106,7 @@ trait MultiSampleQScript extends SummaryQScript {
}
}
- /**
- * Creates a sample file with given suffix
- * @param suffix
- * @return
- */
+ /** Creates a sample file with given suffix */
def createFile(suffix: String) = new File(sampleDir, sampleId + suffix)
/** Returns sample directory */
@@ -158,14 +153,14 @@ trait MultiSampleQScript extends SummaryQScript {
/** Prefix full path with sample and library for jobs that's are created in current state */
override protected[core] def configFullPath: List[String] = {
- val s = currentSample match {
+ val sample = currentSample match {
case Some(s) => "samples" :: s :: Nil
case _ => Nil
}
- val l = currentLib match {
+ val lib = currentLib match {
case Some(l) => "libraries" :: l :: Nil
case _ => Nil
}
- s ::: l ::: super.configFullPath
+ sample ::: lib ::: super.configFullPath
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index 3caaf958c..bf55e0595 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -15,12 +15,12 @@
*/
package nl.lumc.sasc.biopet.core
-import org.apache.log4j.{ PatternLayout, Appender, WriterAppender, FileAppender }
-import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
-import java.io.{ PrintWriter, File }
+import java.io.{File, PrintWriter}
+
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
-import scala.collection.JavaConversions._
+import org.apache.log4j.{PatternLayout, WriterAppender}
+import org.broadinstitute.gatk.queue.util.{Logging => GatkLogging}
/** Wrapper around executable from Queue */
trait PipelineCommand extends MainCommand with GatkLogging {
@@ -33,7 +33,7 @@ trait PipelineCommand extends MainCommand with GatkLogging {
/** Class can be used directly from java with -cp option */
def main(args: Array[String]): Unit = {
- val argsSize = args.size
+ val argsSize = args.length
for (t <- 0 until argsSize) {
if (args(t) == "-config" || args(t) == "--config_file") {
if (t >= argsSize) throw new IllegalStateException("-config needs a value")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
index 8420a107a..5a9786df2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
@@ -7,10 +7,14 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import scala.collection.JavaConversions._
/**
+ * This trait is used for pipelines and extension that use a reference based on one fasta file.
+ * The fasta file can contain multiple contigs.
+ *
* Created by pjvan_thof on 4/6/15.
*/
trait Reference extends Configurable {
+ /** Returns species, default to unknown_species */
def referenceSpecies: String = {
root match {
case r: Reference if r.referenceSpecies != "unknown_species" => r.referenceSpecies
@@ -18,16 +22,17 @@ trait Reference extends Configurable {
}
}
+ /** Return referencename, default to unknown_ref */
def referenceName: String = {
root match {
case r: Reference if r.referenceName != "unknown_ref" => r.referenceName
- case _ => {
+ case _ =>
val default: String = config("default", default = "unknown_ref", path = List("references", referenceSpecies))
config("reference_name", default = default, path = super.configPath)
- }
}
}
+ /** All config values will get a prefix */
override def subPath = {
referenceConfigPath ::: super.subPath
}
@@ -37,8 +42,10 @@ trait Reference extends Configurable {
List("references", referenceSpecies, referenceName)
}
+ /** When set override this on true the pipeline with raise an exception when fai index is not found */
protected def faiRequired = false
+ /** When set override this on true the pipeline with raise an exception when dict index is not found */
protected def dictRequired = false
/** Returns the fasta file */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
index 549b356a1..f0e66c0b0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
@@ -36,20 +36,18 @@ trait ToolCommand extends MainCommand with Logging {
case "error" => logger.setLevel(org.apache.log4j.Level.ERROR)
case _ =>
}
- } text ("Log level") validate { x =>
- x match {
- case "debug" | "info" | "warn" | "error" => success
- case _ => failure("Log level must be <debug/info/warn/error>")
- }
+ } text "Log level" validate {
+ case "debug" | "info" | "warn" | "error" => success
+ case _ => failure("Log level must be <debug/info/warn/error>")
}
opt[Unit]('h', "help") foreach { _ =>
System.err.println(this.usage)
sys.exit(1)
- } text ("Print usage")
+ } text "Print usage"
opt[Unit]('v', "version") foreach { _ =>
System.err.println("Version: " + FullVersion)
sys.exit(1)
- } text ("Print version")
+ } text "Print version"
}
protected type Args <: AbstractArgs
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
index c9a112282..cca4a9086 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
@@ -17,8 +17,6 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-
/**
* Trait for class to let them accept into a Summary
*
@@ -40,7 +38,7 @@ trait Summarizable {
* @param v1 Value of new map
* @param v2 Value of old map
* @param key Key of value
- * @return
+ * @return combined value
*/
def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
throw new IllegalStateException("Merge can not have same key by default")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
index 662ec7048..69e6dfeba 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
@@ -5,6 +5,8 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.ConfigUtils
/**
+ * This class can read in a summary and extract values from it
+ *
* Created by pjvan_thof on 3/26/15.
*/
class Summary(file: File) {
@@ -12,7 +14,7 @@ class Summary(file: File) {
lazy val samples: Set[String] = {
ConfigUtils.getValueFromPath(map, List("samples")) match {
- case Some(samples) => ConfigUtils.any2map(samples).keySet
+ case Some(s) => ConfigUtils.any2map(s).keySet
case _ => Set()
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index 68bb4155c..c59438133 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -23,6 +23,8 @@ import nl.lumc.sasc.biopet.extensions.Md5sum
import scala.collection.mutable
/**
+ * This trait is used for qscript / pipelines that will produce a summary
+ *
* Created by pjvan_thof on 2/14/15.
*/
trait SummaryQScript extends BiopetQScript {
@@ -65,7 +67,7 @@ trait SummaryQScript extends BiopetQScript {
*
* @param summarizable summarizable to add to summary for this pipeline
* @param name Name of module
- * @param sampleId
+ * @param sampleId Id of sample
*/
def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String]): Unit = {
addSummarizable(summarizable, name, sampleId, None)
@@ -76,24 +78,21 @@ trait SummaryQScript extends BiopetQScript {
*
* @param summarizable summarizable to add to summary for this pipeline
* @param name Name of module
- * @param sampleId
- * @param libraryId
+ * @param sampleId Id of sample
+ * @param libraryId Id of libary
*/
def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String], libraryId: Option[String]): Unit = {
if (libraryId.isDefined) require(sampleId.isDefined) // Library always require a sample
summarizables += (name, sampleId, libraryId) -> (summarizable :: summarizables.getOrElse((name, sampleId, libraryId), Nil))
}
- /**
- * Add an other qscript to merge in output summary
- * @param summaryQScript
- */
+ /** Add an other qscript to merge in output summary */
def addSummaryQScript(summaryQScript: SummaryQScript): Unit = {
summaryQScripts :+= summaryQScript
}
/** Add jobs to qscript to execute summary, also add checksum jobs */
- def addSummaryJobs: Unit = {
+ def addSummaryJobs(): Unit = {
val writeSummary = new WriteSummary(this)
def addChecksum(file: File): Unit = {
@@ -119,7 +118,7 @@ trait SummaryQScript extends BiopetQScript {
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList) {
summarizable match {
- case f: BiopetCommandLineFunctionTrait => f.beforeGraph
+ case f: BiopetCommandLineFunctionTrait => f.beforeGraph()
case _ =>
}
}
@@ -141,8 +140,7 @@ trait SummaryQScript extends BiopetQScript {
}
object SummaryQScript {
- import scala.collection.mutable.Map
/** Cache to have no duplicate jobs */
- protected[summary] val md5sumCache: Map[File, File] = Map()
+ protected[summary] val md5sumCache: mutable.Map[File, File] = mutable.Map()
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
index b4cf349d6..546b699e6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
@@ -1,11 +1,11 @@
package nl.lumc.sasc.biopet.core.summary
-import java.math.BigDecimal
-
/**
+ * This case class is used for easy access and calculations on those values
+ *
* Created by pjvan_thof on 4/23/15.
*/
-case class SummaryValue(val value: Option[Any]) {
+case class SummaryValue(value: Option[Any]) {
def this(path: List[String],
summary: Summary,
@@ -18,6 +18,7 @@ case class SummaryValue(val value: Option[Any]) {
})
}
+ //TODO: Calculations are not yet used somewhere, needs more testing
def +(that: SummaryValue): SummaryValue = {
(this.value, that.value) match {
case (Some(a: Double), Some(b)) => SummaryValue(Some(a + b.toString.toDouble))
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index c7b2f7b43..0f573f5af 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -53,9 +53,9 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 4
/** Sets contaminants and adapters when not yet set */
- override def beforeGraph {
+ override def beforeGraph() {
this.jobOutputFile = new File(output.getParentFile, ".fastqc.out")
- this.preProcesExecutable
+ this.preProcessExecutable()
val fastqcDir = new File(executable).getParent
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
index fc1e0a862..afc22bd86 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
@@ -28,8 +28,8 @@ class ConiferExport(val root: Configurable) extends Conifer {
@Output(doc = "Output <sample>.svdzrpkm.bed", shortName = "out", required = true)
var output: File = _
- override def beforeGraph {
- this.preProcesExecutable
+ override def beforeGraph() {
+ this.preProcessExecutable()
}
override def cmdLine = super.cmdLine +
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
index e3a263489..9755ca13a 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -10,6 +10,8 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
/**
+ * With this extension the report is executed within a pipeline
+ *
* Created by pjvan_thof on 3/30/15.
*/
class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
@@ -28,9 +30,9 @@ object ShivaReport extends MultisampleReportBuilder {
List("Samples" -> generateSamplesPage(pageArgs)) ++
(if (regions.isDefined) Map(regions.get) else Map()) ++
Map("Files" -> filesPage,
- "Versions" -> ReportPage(List(), List((
+ "Versions" -> ReportPage(List(), List(
"Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
- ))), Map())
+ )), Map())
),
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
@@ -67,22 +69,22 @@ object ShivaReport extends MultisampleReportBuilder {
}
amplicon match {
- case Some(x: String) => regionPages += (x + " (Amplicon)") -> createPage(x, true)
+ case Some(x: String) => regionPages += (x + " (Amplicon)") -> createPage(x, amplicon = true)
case _ =>
}
roi match {
- case Some(x: String) => regionPages += x -> createPage(x, false)
- case Some(x: List[_]) => x.foreach(x => regionPages += x.toString -> createPage(x.toString, false))
+ case Some(x: String) => regionPages += x -> createPage(x, amplicon = false)
+ case Some(x: List[_]) => x.foreach(x => regionPages += x.toString -> createPage(x.toString, amplicon = false))
case _ =>
}
if (regionPages.nonEmpty) Some("Regions" -> ReportPage(
List(),
- regionPages.map(p => (p._1 -> ReportSection(
+ regionPages.map(p => p._1 -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp",
Map("target" -> p._1.stripSuffix(" (Amplicon)"))
- ))).toList.sortBy(_._1),
+ )).toList.sortBy(_._1),
Map())
)
else None
@@ -156,13 +158,13 @@ object ShivaReport extends MultisampleReportBuilder {
if (libraryLevel) {
for (
- sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+ sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get;
lib <- summary.libraries(sample)
) {
tsvWriter.println(getLine(summary, sample, Some(lib)))
}
} else {
- for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get)) {
+ for (sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get) {
tsvWriter.println(getLine(summary, sample))
}
}
@@ -175,7 +177,7 @@ object ShivaReport extends MultisampleReportBuilder {
plot.ylabel = Some("VCF records")
if (libraryLevel) {
plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
- } else plot.width = Some(200 + (summary.samples.filter(s => sampleId.getOrElse(s) == s).size * 10))
+ } else plot.width = Some(200 + (summary.samples.count(s => sampleId.getOrElse(s) == s) * 10))
plot.runLocal()
}
}
--
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