Commit d76b3f66 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding scala docs

parent 5903aff3
......@@ -19,46 +19,63 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript, BiopetQSc
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/** Template for a multisample pipeline */
class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
/** Location of summary file */
def summaryFile: File = new File(outputDir, "MultisamplePipelineTemplate.summary.json")
/** File to add to the summary */
def summaryFiles: Map[String, File] = Map()
/** Pipeline settings to add to the summary */
def summarySettings: Map[String, Any] = Map()
/** Function to make a sample */
def makeSample(id: String) = new Sample(id)
/** This class will contain jobs and libraries for a sample */
class Sample(sampleId: String) extends AbstractSample(sampleId) {
/** Sample specific files for summary */
def summaryFiles: Map[String, File] = Map()
/** Sample specific stats for summary */
def summaryStats: Map[String, Any] = Map()
/** Function to make a library */
def makeLibrary(id: String) = new Library(id)
/** This class will contain all jobs for a library */
class Library(libId: String) extends AbstractLibrary(libId) {
/** Library specific files for summary */
def summaryFiles: Map[String, File] = Map()
/** Library specific stats for summary */
def summaryStats: Map[String, Any] = Map()
/** Method to add library jobs */
protected def addJobs(): Unit = {
// Library jobs
}
}
/** Method to add sample jobs */
protected def addJobs(): Unit = {
// Sample jobs
}
}
/** Method where multisample jobs are added */
def addMultiSampleJobs(): Unit = {
}
/** This is executed before the script starts */
def init(): Unit = {
}
/** Method where jobs must be added */
def biopetScript() {
}
}
/** Object to let to generate a main method */
object MultisamplePipelineTemplate extends PipelineCommand
\ No newline at end of file
......@@ -20,14 +20,18 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function._
/** Template for a pipeline */
class PipelineTemplate(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
/** This is executed before the script starts */
def init() {
}
/** Method where jobs must be added */
def biopetScript() {
}
}
/** Object to let to generate a main method */
object PipelineTemplate extends PipelineCommand
......@@ -32,6 +32,13 @@ object VcfUtils {
alleles(longestAlleleId)
}
/**
* Method will extend a allele till a new length
* @param bases Allele
* @param newSize New size of allele
* @param fillWith Char to fill gap
* @return
*/
def fillAllele(bases: String, newSize: Int, fillWith: Char = '-'): String = {
bases + (Array.fill[Char](newSize - bases.size)(fillWith)).mkString
}
......
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