From 6ca9d8beb1aefd68bc4fa6a9ada5bed6c009844b Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 5 Mar 2015 10:30:14 +0100
Subject: [PATCH] Update Tabix wrapper
---
.../scala/nl/lumc/sasc/biopet/extensions/Tabix.scala | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
index 0fb2a914d..c32326f34 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
@@ -36,7 +36,7 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
var outputQuery: File = null
@Output(doc = "Output (for indexing)", required = false) // NOTE: it's a def since we can't change the index name ~ it's always input_name + .tbi
- def outputIndex: File = {
+ lazy val outputIndex: File = {
require(input != null, "Input must be defined")
new File(input.toString + ".tbi")
}
@@ -44,7 +44,7 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
@Argument(doc = "Regions to query", required = false)
var regions: List[String] = config("regions", default = List.empty[String])
- var p: String = config("p")
+ var p: Option[String] = config("p")
var s: Option[Int] = config("s")
var b: Option[Int] = config("b")
var e: Option[Int] = config("e")
@@ -67,7 +67,11 @@ class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
private val validFormats: Set[String] = Set("gff", "bed", "sam", "vcf", "psltbl")
override def beforeGraph: Unit = {
- require(validFormats.contains(p), "-p flag must be one of " + validFormats.mkString(", "))
+ p match {
+ case Some(fmt) =>
+ require(validFormats.contains(fmt), "-p flag must be one of " + validFormats.mkString(", "))
+ case None => ;
+ }
}
def cmdLine = {
--
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