From f7f087b2ced6cc89c6e4a20c8b006e711512902d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 26 Jun 2014 08:56:06 +0200
Subject: [PATCH] Added intermediates in creator object
---
.../nl/lumc/sasc/biopet/function/aligners/Star.scala | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
index 0d3026f39..db0c5ff73 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
@@ -82,28 +82,32 @@ class Star(val root:Configurable) extends BiopetCommandLineFunction {
}
object Star {
- def apply(configurable:Configurable, R1:File, R2:File, outputDir:String): Star = {
+ def apply(configurable:Configurable, R1:File, R2:File, outputDir:String, isIntermediate:Boolean = false): Star = {
val star = new Star(configurable)
star.R1 = R1
if (R2 != null) star.R2 = R2
star.outputDir = outputDir
+ star.isIntermediate = isIntermediate
star.afterGraph
return star
}
- def _2pass(configurable:Configurable, R1:File, R2:File, outputDir:String) : (File, List[Star]) = {
+ def _2pass(configurable:Configurable, R1:File, R2:File, outputDir:String, isIntermediate:Boolean = false) : (File, List[Star]) = {
val outDir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, outDir + "aln-pass1/")
+ starCommand_pass1.isIntermediate = isIntermediate
starCommand_pass1.afterGraph
val starCommand_reindex = new Star(configurable)
starCommand_reindex.sjdbFileChrStartEnd = starCommand_pass1.outputTab
starCommand_reindex.outputDir = outDir + "re-index/"
starCommand_reindex.runmode = "genomeGenerate"
+ starCommand_reindex.isIntermediate = isIntermediate
starCommand_reindex.afterGraph
val starCommand_pass2 = Star(configurable, R1, if (R2 != null) R2 else null, outDir + "aln-pass2/")
starCommand_pass2.genomeDir = starCommand_reindex.outputDir
+ starCommand_pass2.isIntermediate = isIntermediate
starCommand_pass2.afterGraph
return (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))
--
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