From 23abce49eb95b8d9cef46e941385f7d5fdc19c4c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 16:25:38 +0100
Subject: [PATCH] Change name checkExecutable to preProcesExecutable
---
.../sasc/biopet/core/BiopetCommandLineFunctionTrait.scala | 8 ++++----
.../scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala | 2 +-
.../sasc/biopet/extensions/conifer/ConiferExport.scala | 2 +-
4 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index f0c2f37c6..99a5667d7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -57,7 +57,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
* Set default output file, threads and vmem for current job
*/
override def freezeFieldValues() {
- checkExecutable
+ preProcesExecutable
beforeGraph
if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
@@ -77,7 +77,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/**
* Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
*/
- protected[core] def checkExecutable {
+ protected[core] def preProcesExecutable {
if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
try if (executable != null) {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
@@ -119,7 +119,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
* executes checkExecutable method and fill job report
*/
final protected def preCmdInternal {
- checkExecutable
+ preProcesExecutable
beforeCmd
@@ -170,7 +170,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/** Get version from cache otherwise execute the version command */
def getVersion: String = {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
- checkExecutable
+ preProcesExecutable
if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
return BiopetCommandLineFunctionTrait.versionCache(executable)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 807555d60..3ae6780e4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -71,7 +71,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
}
for (function <- functions) function match {
case f: BiopetCommandLineFunctionTrait => {
- f.checkExecutable
+ f.preProcesExecutable
f.beforeGraph
f.commandLine
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 8edf474e7..05867d694 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -49,7 +49,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 4
override def beforeGraph {
- this.checkExecutable
+ this.preProcesExecutable
val fastqcDir = new File(executable).getParent
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
index c7b816953..fc1e0a862 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
@@ -29,7 +29,7 @@ class ConiferExport(val root: Configurable) extends Conifer {
var output: File = _
override def beforeGraph {
- this.checkExecutable
+ this.preProcesExecutable
}
override def cmdLine = super.cmdLine +
--
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