From c1f9f9e8cb965049eee78a3928911b0ba608af10 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 18 Sep 2015 11:01:53 +0200
Subject: [PATCH] Sync with develop and fix build issues
---
.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala | 5 +++--
.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala | 4 ++--
.../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala | 0
.../sasc/biopet/extensions/tools/BastyGenerateFasta.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala | 2 +-
.../biopet/extensions/tools/BedtoolsCoverageToCounts.scala | 2 +-
.../lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala | 4 ++--
.../nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala | 4 ++--
.../nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala | 4 ++--
.../nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala | 2 +-
.../lumc/sasc/biopet/extensions/tools/SageCountFastq.scala | 2 +-
.../sasc/biopet/extensions/tools/SageCreateLibrary.scala | 2 +-
.../sasc/biopet/extensions/tools/SageCreateTagCounts.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala | 2 +-
22 files changed, 27 insertions(+), 26 deletions(-)
rename public/{biopet-framework => biopet-core}/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala (93%)
rename public/{biopet-framework => biopet-core}/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala (100%)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index 2f098dfaa..44a7e780f 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -18,7 +18,8 @@ package nl.lumc.sasc.biopet.core
import java.io.{ File, FileInputStream }
import java.security.MessageDigest
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
@@ -110,7 +111,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
if (executableToCanonicalPath) executable = file.getCanonicalPath
else executable = file.getAbsolutePath
} else {
- BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
+ Logging.addError("executable: '" + executable + "' not found, please check config")
}
BiopetCommandLineFunction.executableCache += oldExecutable -> executable
BiopetCommandLineFunction.executableCache += executable -> executable
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
similarity index 93%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
index 8cd0737ac..40b546bde 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.core
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* This class can pipe multiple BiopetCommandFunctions to 1 job
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
rename to public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
index 9b0020ae2..bc1d67226 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
@@ -55,7 +55,7 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with
reference = referenceFasta()
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
optional("--inputVcf", inputVcf) +
optional("--bamFile", bamFile) +
optional("--outputVariants", outputVariants) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
index bab2f7c0a..f7f00d0f9 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
@@ -38,7 +38,7 @@ class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 1.0
- override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
+ override def cmdLine = super.cmdLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
}
object BedToInterval {
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
index 817b6d3f2..00a77a5e9 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
@@ -32,7 +32,7 @@ class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntio
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
index ff06bc963..5dc69cb07 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
@@ -37,7 +37,7 @@ class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Sum
override def defaultCoreMemory = 6.0
- override def commandLine = super.commandLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
+ override def cmdLine = super.cmdLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
def summaryFiles: Map[String, File] = Map()
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
index df7e32e19..734804844 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
@@ -37,7 +37,7 @@ class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 4.0
/** * Generate command to execute */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
repeat("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
index 90100c8e7..4d56c8e49 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
@@ -55,8 +55,8 @@ class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summariz
override def defaultCoreMemory = 4.0
// executed command line
- override def commandLine =
- super.commandLine +
+ override def cmdLine =
+ super.cmdLine +
required("-r", refFastq) +
required("-i", inputFastq1) +
required("-j", inputFastq2) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
index eedb51fdd..504c7cb7c 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
@@ -43,7 +43,7 @@ class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
repeat("-I", input) +
required("-o", output) +
required("-R", reference)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
index 96a421db3..15ca55b6a 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
@@ -65,8 +65,8 @@ class MergeTables(val root: Configurable) extends ToolCommandFuntion {
var delimiter: Option[String] = config("delimiter")
// executed command line
- override def commandLine =
- super.commandLine +
+ override def cmdLine =
+ super.cmdLine +
required("-i", idColumnIndices.mkString(",")) +
required("-a", valueColumnIndex) +
optional("-n", idColumnName) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
index 5a3e1e3f2..212641116 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
@@ -66,14 +66,14 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
}
}
- override def commandLine = {
+ override def cmdLine = {
(if (inputMpileup == null) {
val samtoolsMpileup = new SamtoolsMpileup(this)
samtoolsMpileup.reference = referenceFasta()
samtoolsMpileup.input = List(inputBam)
samtoolsMpileup.cmdPipe + " | "
} else "") +
- super.commandLine +
+ super.cmdLine +
required("-o", output) +
optional("--minDP", minDP) +
optional("--minAP", minAP) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
index 302aa1158..dca36baf3 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
@@ -44,7 +44,7 @@ class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
* Creates command to execute extension
* @return
*/
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-i", inputFastq) +
required("-o", outputFastq) +
optional("-s", prefixSeq)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
index 2ee9d97e1..0e71324db 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
@@ -32,7 +32,7 @@ class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output)
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
index 4b287d2ce..a2d79430f 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
@@ -44,7 +44,7 @@ class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
optional("--tag", tag) +
optional("--length", length) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
index d0779973b..30e7f524f 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
@@ -44,7 +44,7 @@ class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("--tagLib", tagLib) +
optional("--countSense", countSense) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
index cc7a8e6ed..3f1cf95a4 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
@@ -24,7 +24,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizab
override def defaultCoreMemory = 2.5
- override def commandLine = super.commandLine + required("-i", input) + required("-o", output)
+ override def cmdLine = super.cmdLine + required("-i", input) + required("-o", output)
def summaryStats: Map[String, Any] = {
val map = ConfigUtils.fileToConfigMap(output)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
index 558c93f85..f42f635be 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
@@ -20,7 +20,7 @@ class SquishBed(val root: Configurable) extends ToolCommandFuntion {
var strandSensitive: Boolean = config("strandSensitive", default = false)
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output) +
conditional(strandSensitive, "-s")
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
index 60d550532..06af56f02 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
@@ -38,7 +38,7 @@ class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 3.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", inputVcf) +
required("-o", outputVcf) +
optional("--minSampleDepth", minSampleDepth) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
index 3fd09a67f..d0024681b 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
@@ -69,7 +69,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summariza
}
/** Creates command to execute extension */
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", outputDir) +
repeat("--infoTag", infoTags) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
index 5ab877502..e956f5c93 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
@@ -50,7 +50,7 @@ class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
if (fields.isEmpty) throw new IllegalArgumentException("No fields found for VcfWithVcf")
}
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", input) +
required("-o", output) +
required("-s", secondaryVcf) +
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
index 4379b990d..229f39628 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
@@ -45,7 +45,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
override def defaultCoreMemory = 4.0
- override def commandLine = super.commandLine +
+ override def cmdLine = super.cmdLine +
required("-I", inputVCF) +
required("-O", outputVcf) +
required("-m", mode) +
--
GitLab