From 044fe79f45fef19909972bfb2d891a89f72fcb78 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 18 Jul 2014 15:53:10 +0200
Subject: [PATCH] Library fix for Queue/GATK 3.2
---
.../lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala | 2 +-
.../sasc/biopet/function/picard/CollectGcBiasMetrics.scala | 2 +-
.../biopet/function/picard/CollectInsertSizeMetrics.scala | 2 +-
.../nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala | 4 ++--
4 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala
index 4e4fdad0f..f4ab141b8 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CalculateHsMetrics.scala
@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class CalculateHsMetrics(val root:Configurable) extends Picard {
- javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"
+ javaMainClass = "picard.analysis.directed.CalculateHsMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = _
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala
index 490875d00..7da1952a9 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectGcBiasMetrics.scala
@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class CollectGcBiasMetrics(val root:Configurable) extends Picard {
- javaMainClass = "net.sf.picard.analysis.CollectGcBiasMetrics"
+ javaMainClass = "picard.analysis.CollectGcBiasMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: Seq[File] = Nil
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectInsertSizeMetrics.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectInsertSizeMetrics.scala
index 63535770b..a2dc471f2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectInsertSizeMetrics.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/CollectInsertSizeMetrics.scala
@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class CollectInsertSizeMetrics(val root:Configurable) extends Picard {
- javaMainClass = "net.sf.picard.analysis.CollectInsertSizeMetrics"
+ javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = _
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala
index 6dfeca85a..4789452bd 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/MarkDuplicates.scala
@@ -5,8 +5,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class MarkDuplicates(val root:Configurable) extends Picard {
- javaMainClass = "net.sf.picard.sam.MarkDuplicates"
-
+ javaMainClass = "picard.sam.MarkDuplicates"
+
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: List[File] = Nil
--
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