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Commit d81585ca authored by Peter van 't Hof's avatar Peter van 't Hof
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Adding scala docs

parent 7908eb1d
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @ d81585ca
......@@ -13,6 +13,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
qscript =>
def this() = this(null)
/** Make variantcalling submodule, this with the gatk modes in there */
override def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
if (multisample) new ShivaVariantcalling(qscript) {
override def namePrefix = "multisample"
......@@ -24,10 +25,18 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
}
}
/** Makes a sample */
override def makeSample(id: String) = new this.Sample(id)
/** Class will generate sample jobs */
class Sample(sampleId: String) extends super.Sample(sampleId) {
/** Makes a library */
override def makeLibrary(id: String) = new this.Library(id)
/** Class will generate library jobs */
class Library(libId: String) extends super.Library(libId) {
/** This will adds preprocess steps, gatk indel realignment and base recalibration is included here */
override def preProcess(input: File): Option[File] = {
val useIndelRealigner: Boolean = config("use_indel_realign", default = true)
val useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
......@@ -47,6 +56,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
}
}
/** This methods will add double preprocess steps, with GATK indel realignment */
override protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
if (input.size <= 1) super.addDoublePreProcess(input)
else super.addDoublePreProcess(input, true).collect {
......@@ -60,6 +70,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
}
}
/** Adds indel realignment jobs */
def addIndelRealign(inputBam: File, dir: File, isIntermediate: Boolean): File = {
val realignerTargetCreator = RealignerTargetCreator(this, inputBam, dir)
realignerTargetCreator.isIntermediate = true
......@@ -72,6 +83,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
return indelRealigner.o
}
/** Adds base recalibration jobs */
def addBaseRecalibrator(inputBam: File, dir: File, isIntermediate: Boolean): File = {
val baseRecalibrator = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal"))
......@@ -98,4 +110,5 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
}
}
/** This object give a default main methods for this pipeline */
object Shiva extends PipelineCommand
\ No newline at end of file
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
View file @ d81585ca
......@@ -13,6 +13,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
qscript =>
def this() = this(null)
/** Will generate all available variantcallers */
override def callersList = {
new HaplotypeCallerGvcf ::
new HaplotypeCallerAllele ::
......@@ -22,6 +23,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
super.callersList
}
/** Default mode for the haplotypecaller */
class HaplotypeCaller extends Variantcaller {
val name = "haplotypecaller"
protected val defaultPrio = 1
......@@ -36,6 +38,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
}
}
/** Default mode for UnifiedGenotyper */
class UnifiedGenotyper extends Variantcaller {
val name = "unifiedgenotyper"
protected val defaultPrio = 20
......@@ -50,6 +53,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
}
}
/** Allele mode for Haplotypecaller */
class HaplotypeCallerAllele extends Variantcaller {
val name = "haplotypecaller_allele"
protected val defaultPrio = 5
......@@ -66,6 +70,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
}
}
/** Allele mode for GenotyperAllele */
class UnifiedGenotyperAllele extends Variantcaller {
val name = "unifiedgenotyper_allele"
protected val defaultPrio = 9
......@@ -82,6 +87,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
}
}
/** Gvcf mode for haplotypecaller */
class HaplotypeCallerGvcf extends Variantcaller {
val name = "haplotypecaller_gvcf"
protected val defaultPrio = 5
......@@ -104,4 +110,5 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
}
}
/** object to add default main method to pipeline */
object ShivaVariantcalling extends PipelineCommand
\ No newline at end of file
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @ d81585ca
......@@ -11,4 +11,5 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
def this() = this(null)
}
/** This object give a default main method to the pipelines */
object Shiva extends PipelineCommand
\ No newline at end of file
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @ d81585ca
......@@ -12,21 +12,25 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import scala.collection.JavaConversions._
/**
* This is a trait for the Shiva pipeline
*
* Created by pjvan_thof on 2/26/15.
*/
trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
qscript =>
/** Executed before running the script */
def init: Unit = {
}
/** Method to add jobs */
def biopetScript: Unit = {
addSamplesJobs()
addSummaryJobs
}
/** Method to make the variantcalling submodule of shiva */
def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
if (multisample) new ShivaVariantcalling(qscript) {
override def namePrefix = "multisample"
......@@ -38,27 +42,43 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
}
}
/** Method to make a sample */
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
/** Class that will generate jobs for a sample */
class Sample(sampleId: String) extends AbstractSample(sampleId) {
/** Sample specific files to add to summary */
def summaryFiles: Map[String, File] = {
preProcessBam match {
case Some(preProcessBam) => Map("bamFile" -> preProcessBam)
case _ => Map()
}
}
//TODO: Add summary
/** Sample specific stats to add to summary */
def summaryStats: Map[String, Any] = Map()
/** Method to make a library */
def makeLibrary(id: String) = new Library(id)
/** Class to generate jobs for a library */
class Library(libId: String) extends AbstractLibrary(libId) {
/** Library specific files to add to the summary */
def summaryFiles: Map[String, File] = {
(bamFile, preProcessBam) match {
case (Some(bamFile), Some(preProcessBam)) => Map("bamFile" -> bamFile, "preProcessBam" -> preProcessBam)
case (Some(bamFile), _) => Map("bamFile" -> bamFile)
case _ => Map()
}
}
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
/** Library specific stats to add to summary */
def summaryStats: Map[String, Any] = Map()
/** Method to execute library preprocess */
def preProcess(input: File): Option[File] = None
/** Method to make the mapping submodule */
def makeMapping = {
val mapping = new Mapping(qscript)
mapping.sampleId = Some(sampleId)
......@@ -87,6 +107,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
Some(makeVariantcalling(multisample = false))
} else None
/** This will add jobs for this library */
def addJobs(): Unit = {
(config.contains("R1"), config.contains("bam")) match {
case (true, _) => mapping.foreach(mapping => {
......@@ -165,6 +186,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
}
}
/** This will add jobs for the double preprocessing */
protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
if (input == Nil) None
else if (input.tail == Nil) {
......@@ -202,6 +224,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
Some(makeVariantcalling(multisample = true))
} else None
/** This will add sample jobs */
def addJobs(): Unit = {
addPerLibJobs()
......@@ -232,6 +255,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
Some(makeVariantcalling(multisample = true))
} else None
/** This will add the mutisample variantcalling */
def addMultiSampleJobs(): Unit = {
variantcalling.foreach(vc => {
vc.outputDir = new File(outputDir, "variantcalling")
......@@ -243,9 +267,12 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
})
}
/** Location of summary file */
def summaryFile = new File(outputDir, "Shiva.summary.json")
/** Settings of pipeline for summary */
def summarySettings = Map()
/** Files for the summary */
def summaryFiles = Map()
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @ d81585ca
......@@ -24,6 +24,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
@Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
var inputBams: List[File] = Nil
/** Name prefix, can override this methods if neeeded */
def namePrefix: String = {
(sampleId, libId) match {
case (Some(sampleId), Some(libId)) => sampleId + "-" + libId
......@@ -32,14 +33,18 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
}
}
/** Executed before script */
def init: Unit = {
}
/** Final merged output files of all variantcaller modes */
def finalFile = new File(outputDir, namePrefix + ".final.vcf.gz")
def biopetScript: Unit = {
val configCallers: Set[String] = config("variantcallers")
/** Variantcallers requested by the config */
protected val configCallers: Set[String] = config("variantcallers")
/** This will add jobs for this pipeline */
def biopetScript: Unit = {
for (cal <- configCallers) {
if (!callersList.exists(_.name == cal))
BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
......@@ -77,21 +82,36 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
addSummaryJobs
}
/** Will generate all available variantcallers */
protected def callersList: List[Variantcaller] = List(new Freebayes, new RawVcf, new Bcftools)
/** General trait for a variantcaller mode */
trait Variantcaller {
/** Name of mode, this should also be used in the config */
val name: String
/** Output dir for this mode */
def outputDir = new File(qscript.outputDir, name)
/** Prio in merging in the final file */
protected val defaultPrio: Int
/** Prio from the config */
lazy val prio: Int = config("prio_" + name, default = defaultPrio)
/** This should add the variantcaller jobs */
def addJobs()
/** Final output file of this mode */
def outputFile: File
}
/** default mode of freebayes */
class Freebayes extends Variantcaller {
val name = "freebayes"
protected val defaultPrio = 7
/** Final output file of this mode */
def outputFile = new File(outputDir, namePrefix + ".freebayes.vcf.gz")
def addJobs() {
......@@ -101,7 +121,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
fb.isIntermediate = true
add(fb)
//TODO: need piping for this
//TODO: need piping for this, see also issue #114
val bz = new Bgzip(qscript)
bz.input = List(fb.outputVcf)
bz.output = outputFile
......@@ -114,10 +134,12 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
}
}
/** default mode of bcftools */
class Bcftools extends Variantcaller {
val name = "bcftools"
protected val defaultPrio = 8
/** Final output file of this mode */
def outputFile = new File(outputDir, namePrefix + ".bcftools.vcf.gz")
def addJobs() {
......@@ -143,10 +165,12 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
}
}
/** Makes a vcf file from a mpileup without statistics */
class RawVcf extends Variantcaller {
val name = "raw"
protected val defaultPrio = 999
/** Final output file of this mode */
def outputFile = new File(outputDir, namePrefix + ".raw.vcf.gz")
def addJobs() {
......@@ -179,10 +203,13 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
}
}
/** Location of summary file */
def summaryFile = new File(outputDir, "ShivaVariantcalling.summary.json")
def summarySettings = Map()
/** Settings for the summary */
def summarySettings = Map("variantcallers" -> configCallers.toList)
/** Files for the summary */
def summaryFiles: Map[String, File] = {
val callers: Set[String] = config("variantcallers")
callersList.filter(x => callers.contains(x.name)).map(x => (x.name -> x.outputFile)).toMap + ("final" -> finalFile)
......
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