From b938c1b8e3dbcecdf97f65a9a7591d58a56e3404 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Nov 2015 21:08:37 +0100
Subject: [PATCH] Added init version of dependency debug mode
---
.../lumc/sasc/biopet/core/BiopetQScript.scala | 2 +
.../sasc/biopet/core/WriteDependencies.scala | 39 +++++++++++++++++++
2 files changed, 41 insertions(+)
create mode 100644 public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 4cbcfdb68..9bc18a938 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -102,6 +102,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
case _ => reportClass.foreach(add(_))
}
+ if (logger.isDebugEnabled) WriteDependencies.writeDependencies(functions, new File(outputDir, s".log/${qSettings.runName}.deps.json"))
+
Logging.checkErrors()
}
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
new file mode 100644
index 000000000..a14477be6
--- /dev/null
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
@@ -0,0 +1,39 @@
+package nl.lumc.sasc.biopet.core
+
+import java.io.{File, PrintWriter}
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.function.{CommandLineFunction, QFunction}
+import scala.collection.mutable
+
+/**
+ * Created by pjvanthof on 06/11/15.
+ */
+object WriteDependencies {
+ val functionNames: mutable.Map[QFunction, String] = mutable.Map()
+
+ def createFunctionNames(functions: Seq[QFunction]): Unit = {
+ val cache: mutable.Map[String, Int] = mutable.Map()
+ for (function <- functions) {
+ val baseName = function match {
+ case f: BiopetCommandLineFunction => f.configName
+ case f => f.getClass.getSimpleName
+ }
+ cache += baseName -> (cache.getOrElse(baseName, 0) + 1)
+ functionNames += function -> (s"$baseName-${cache(baseName)}")
+ }
+ }
+
+ def writeDependencies(functions: Seq[QFunction], outputFile: File): Unit = {
+ createFunctionNames(functions)
+ val writer = new PrintWriter(outputFile)
+ val jobs = functionNames.map { case (f, name) => name -> Map("command" -> (f match {
+ case cmd: CommandLineFunction => cmd.commandLine
+ case _ => None
+ }), "intermediate" -> f.isIntermediate) }
+
+ writer.println(ConfigUtils.mapToJson(jobs.toMap).spaces2)
+ writer.close()
+ }
+
+}
--
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