From d49e8e659b454df3c710e0418f509212b35c3409 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 15 Apr 2015 16:29:27 +0200
Subject: [PATCH] Safer class name, now checked by the compiler
---
.../sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala | 2 +-
.../sasc/biopet/extensions/picard/CalculateHsMetrics.scala | 2 +-
.../extensions/picard/CollectAlignmentSummaryMetrics.scala | 2 +-
.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala | 2 +-
.../biopet/extensions/picard/CollectInsertSizeMetrics.scala | 2 +-
.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala | 3 ++-
.../nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala | 2 +-
12 files changed, 13 insertions(+), 12 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
index 232cbc241..bd1c2ff70 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
@@ -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 = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
index 314418afa..7eb26f237 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
@@ -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 = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index 541ee75b8..66697a0b2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -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 = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index f93dc4aa7..c1197cc21 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index 6ef7bd62e..bfe20ec89 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
index 6629fae64..dd922fce5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
@@ -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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
index 89ceb13e3..1d7671a4f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
@@ -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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index 52777a467..318b1e7f4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
index ef3f358ab..3c850f374 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
@@ -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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
index cb29b2e1e..f90a08938 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
@@ -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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
index 96bfdf422..d997e472f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
@@ -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 = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index 8d2946291..fecc71075 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -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 = _
--
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