Commit 5903aff3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding scala docs

parent 24749608
......@@ -25,7 +25,7 @@ import scala.io.Source
/**
* General picard extension
*
* This is based on using class files directly from the jar
* This is based on using class files directly from the jar, if needed other picard jar can be used
*/
abstract class Picard extends BiopetJavaCommandLineFunction {
override def subPath = "picard" :: super.subPath
......
......@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/** General Sambamba extension */
abstract class Sambamba extends BiopetCommandLineFunction {
override val defaultVmem = "4G"
override val defaultThreads = 2
......
......@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for sambemba flagstat */
class SambambaFlagstat(val root: Configurable) extends Sambamba {
override val defaultThreads = 2
......@@ -28,6 +29,7 @@ class SambambaFlagstat(val root: Configurable) extends Sambamba {
@Output(doc = "output File")
var output: File = _
/** Returns command to execute */
def cmdLine = required(executable) +
required("flagstat") +
optional("-t", nCoresRequest) +
......@@ -35,24 +37,3 @@ class SambambaFlagstat(val root: Configurable) extends Sambamba {
" > " +
required(output)
}
object SambambaFlagstat {
def apply(root: Configurable, input: File, output: File): SambambaFlagstat = {
val flagstat = new SambambaFlagstat(root)
flagstat.input = input
flagstat.output = output
return flagstat
}
def apply(root: Configurable, input: File, outputDir: String): SambambaFlagstat = {
val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
val outputFile = new File(dir + swapExtension(input.getName))
return apply(root, input, outputFile)
}
def apply(root: Configurable, input: File): SambambaFlagstat = {
return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
}
private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".flagstat"
}
\ No newline at end of file
......@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for sambemba index */
class SambambaIndex(val root: Configurable) extends Sambamba {
override val defaultThreads = 2
......@@ -28,30 +29,10 @@ class SambambaIndex(val root: Configurable) extends Sambamba {
@Output(doc = "Output .bai file to")
var output: File = _
/** Returns command to execute */
def cmdLine = required(executable) +
required("index") +
optional("-t", nCoresRequest) +
required(input) +
required(output)
}
object SambambaIndex {
def apply(root: Configurable, input: File, output: File): SambambaIndex = {
val flagstat = new SambambaIndex(root)
flagstat.input = input
flagstat.output = output
return flagstat
}
def apply(root: Configurable, input: File, outputDir: String): SambambaIndex = {
val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
val outputFile = new File(dir + swapExtension(input.getName))
return apply(root, input, outputFile)
}
def apply(root: Configurable, input: File): SambambaIndex = {
return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
}
private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".bam.bai"
}
\ No newline at end of file
......@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for sambemba markdup */
class SambambaMarkdup(val root: Configurable) extends Sambamba {
override val defaultThreads = 4
......@@ -36,6 +37,7 @@ class SambambaMarkdup(val root: Configurable) extends Sambamba {
val overflow_list_size: Option[Int] = config("overflow-list-size", default = 200000)
val io_buffer_size: Option[Int] = config("io-buffer-size", default = 128)
/** Returns command to execute */
def cmdLine = required(executable) +
required("markdup") +
conditional(remove_duplicates, "--remove-duplicates") +
......@@ -47,24 +49,3 @@ class SambambaMarkdup(val root: Configurable) extends Sambamba {
required(input) +
required(output)
}
object SambambaMarkdup {
def apply(root: Configurable, input: File, output: File): SambambaMarkdup = {
val flagstat = new SambambaMarkdup(root)
flagstat.input = input
flagstat.output = output
return flagstat
}
def apply(root: Configurable, input: File, outputDir: String): SambambaMarkdup = {
val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
val outputFile = new File(dir + swapExtension(input.getName))
return apply(root, input, outputFile)
}
def apply(root: Configurable, input: File): SambambaMarkdup = {
return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
}
private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".bam.bai"
}
\ No newline at end of file
......@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for sambemba merge */
class SambambaMerge(val root: Configurable) extends Sambamba {
override val defaultThreads = 4
......@@ -31,6 +32,7 @@ class SambambaMerge(val root: Configurable) extends Sambamba {
// @doc: compression_level 6 is average, 0 = no compression, 9 = best
val compression_level: Option[Int] = config("compression_level", default = 6)
/** Returns command to execute */
def cmdLine = required(executable) +
required("merge") +
optional("-t", nCoresRequest) +
......@@ -38,36 +40,3 @@ class SambambaMerge(val root: Configurable) extends Sambamba {
required(output) +
repeat("", input)
}
object SambambaMerge {
def apply(root: Configurable, input: List[File], output: File): SambambaMerge = {
val flagstat = new SambambaMerge(root)
flagstat.input = input
flagstat.output = output
return flagstat
}
def apply(root: Configurable, input: List[File], outputDir: String): SambambaMerge = {
val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
val outputFile = new File(dir + swapExtension(input.head.getName))
return apply(root, input, outputFile)
}
def apply(root: Configurable, input: List[File]): SambambaMerge = {
return apply(root, input, new File(swapExtension(input.head.getAbsolutePath)))
}
private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".merge.bam"
}
//
//object MergeSamFiles {
// def apply(root: Configurable, input: List[File], outputDir: String, sortOrder: String = null): MergeSamFiles = {
// val mergeSamFiles = new MergeSamFiles(root)
// mergeSamFiles.input = input
// mergeSamFiles.output = new File(outputDir, input.head.getName.stripSuffix(".bam").stripSuffix(".sam") + ".merge.bam")
// if (sortOrder == null) mergeSamFiles.sortOrder = "coordinate"
// else mergeSamFiles.sortOrder = sortOrder
// return mergeSamFiles
// }
//}
\ No newline at end of file
......@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/** General class for samtools extensions */
abstract class Samtools extends BiopetCommandLineFunction {
override def subPath = "samtools" :: super.subPath
executable = config("exe", default = "samtools")
......
......@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for samtools flagstat */
class SamtoolsFlagstat(val root: Configurable) extends Samtools {
@Input(doc = "Bam File")
var input: File = _
......@@ -26,6 +27,7 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
@Output(doc = "output File")
var output: File = _
/** Returns command to execute */
def cmdLine = required(executable) + required("flagstat") + required(input) + " > " + required(output)
}
......
......@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for samtools mpileup */
class SamtoolsMpileup(val root: Configurable) extends Samtools {
@Input(doc = "Bam File")
var input: File = _
......@@ -45,6 +46,8 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
conditional(disableBaq, "-B")
def cmdPipeInput = cmdBase + "-"
def cmdPipe = cmdBase + required(input)
/** Returns command to execute */
def cmdLine = cmdPipe + " > " + required(output)
}
......
......@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for samtools view */
class SamtoolsView(val root: Configurable) extends Samtools {
@Input(doc = "Bam File")
var input: File = _
......@@ -37,6 +38,8 @@ class SamtoolsView(val root: Configurable) extends Samtools {
conditional(h, "-h")
def cmdPipeInput = cmdBase + "-"
def cmdPipe = cmdBase + required(input)
/** Returns command to execute */
def cmdLine = cmdPipe + " > " + required(output)
}
......
......@@ -17,9 +17,7 @@ package nl.lumc.sasc.biopet.extensions.seqtk
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/**
* Abstract class for all seqtk wrappers.
*/
/** Abstract class for all seqtk wrappers. */
abstract class Seqtk extends BiopetCommandLineFunction {
override def subPath = "seqtk" :: super.subPath
executable = config("exe", default = "seqtk", freeVar = true)
......
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