Commit d49e8e65 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Safer class name, now checked by the compiler

parent 61232d12
......@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard AddOrReplaceReadGroups */
class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.AddOrReplaceReadGroups"
javaMainClass = new picard.sam.AddOrReplaceReadGroups().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: File = _
......
......@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard CalculateHsMetrics */
class CalculateHsMetrics(val root: Configurable) extends Picard {
javaMainClass = "picard.analysis.directed.CalculateHsMetrics"
javaMainClass = new picard.analysis.directed.CalculateHsMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = _
......
......@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard CollectAlignmentSummaryMetrics */
class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
javaMainClass = "picard.analysis.CollectAlignmentSummaryMetrics"
javaMainClass = new picard.analysis.CollectAlignmentSummaryMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = _
......
......@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard CollectGcBiasMetrics */
class CollectGcBiasMetrics(val root: Configurable) extends Picard {
javaMainClass = "picard.analysis.CollectGcBiasMetrics"
javaMainClass = new picard.analysis.CollectGcBiasMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: Seq[File] = Nil
......
......@@ -24,7 +24,7 @@ import scala.collection.immutable.Nil
/** Extension for picard CollectInsertSizeMetrics */
class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable {
javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
javaMainClass = new picard.analysis.CollectInsertSizeMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = null
......
......@@ -26,7 +26,7 @@ import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
*/
class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summarizable {
javaMainClass = "picard.analysis.CollectRnaSeqMetrics"
javaMainClass = new picard.analysis.CollectRnaSeqMetrics().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze", required = true)
var input: File = null
......
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class GatherBamFiles(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.GatherBamFiles"
javaMainClass = new picard.sam.GatherBamFiles().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: List[File] = Nil
......
......@@ -22,7 +22,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard MarkDuplicates */
class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
javaMainClass = "picard.sam.MarkDuplicates"
javaMainClass = new picard.sam.MarkDuplicates().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: List[File] = Nil
......
......@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard MergeSamFiles */
class MergeSamFiles(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.MergeSamFiles"
javaMainClass = new picard.sam.MergeSamFiles().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: List[File] = Nil
......
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class ReorderSam(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.ReorderSam"
javaMainClass = new picard.sam.ReorderSam().getClass.getName
@Input(doc = "Input SAM or BAM file", required = true)
var input: File = null
......
......@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard SamToFastq */
class SamToFastq(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.SamToFastq"
javaMainClass = new picard.sam.SamToFastq().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: File = _
......
......@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
/** Extension for picard SortSam */
class SortSam(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.SortSam"
javaMainClass = new picard.sam.SortSam().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: File = _
......
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