From 2af46d82e538afe56b5e2415ff9ab7abd6032b8a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 5 Apr 2016 12:57:21 +0200
Subject: [PATCH] Refactor Reference so dict and fai file becomes accessable as
a method
---
.../core/BiopetCommandLineFunction.scala | 9 +++++++
.../nl/lumc/sasc/biopet/core/Reference.scala | 26 +++++++++----------
2 files changed, 22 insertions(+), 13 deletions(-)
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 a413c8bad..23122f1e3 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
@@ -73,6 +73,15 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
def beforeGraph() {}
override def freezeFieldValues() {
+
+ this match {
+ case r:Reference =>
+ if (r.dictRequired) deps :+= r.referenceDict
+ if (r.faiRequired) deps :+= r.referenceFai
+ deps = deps.distinct
+ case _ =>
+ }
+
preProcessExecutable()
beforeGraph()
internalBeforeGraph()
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
index 6a39ca3eb..f00de9e17 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
@@ -61,25 +61,25 @@ trait Reference extends Configurable {
}
/** When set override this on true the pipeline with raise an exception when fai index is not found */
- protected def faiRequired = false
+ def faiRequired = false
/** When set override this on true the pipeline with raise an exception when dict index is not found */
- protected def dictRequired = this.isInstanceOf[Summarizable] || this.isInstanceOf[SummaryQScript]
+ def dictRequired = this.isInstanceOf[Summarizable] || this.isInstanceOf[SummaryQScript]
+
+ /** Returns the dict file belonging to the fasta file */
+ def referenceDict = new File(referenceFasta().getAbsolutePath
+ .stripSuffix(".fa")
+ .stripSuffix(".fasta")
+ .stripSuffix(".fna") + ".dict")
+
+ /** Returns the fai file belonging to the fasta file */
+ def referenceFai = new File(referenceFasta().getAbsolutePath + ".fai")
/** Returns the fasta file */
def referenceFasta(): File = {
val file: File = config("reference_fasta")
- if (config.contains("reference_fasta")) {
- checkFasta(file)
-
- val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta").stripSuffix(".fna") + ".dict")
- val fai = new File(file.getAbsolutePath + ".fai")
-
- this match {
- case c: BiopetCommandLineFunction => c.deps :::= dict :: fai :: Nil
- case _ =>
- }
- } else {
+ if (config.contains("reference_fasta")) checkFasta(file)
+ else {
val defaults = ConfigUtils.mergeMaps(this.defaults, this.internalDefaults)
def getReferences(map: Map[String, Any]): Set[(String, String)] = (for (
--
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