From f861ddbb7a7a95afd7311f19aa9c1a091302a72b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Nov 2015 12:24:28 +0100
Subject: [PATCH] Fix null pointer on missing values
---
.../biopet/pipelines/gentrap/Gentrap.scala | 31 +++++++++++++------
1 file changed, 22 insertions(+), 9 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 724470df1..298fd7770 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -19,25 +19,24 @@ import java.io.File
import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.utils.config._
import nl.lumc.sasc.biopet.core.summary._
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
+import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
import nl.lumc.sasc.biopet.extensions.{ HtseqCount, Ln }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{ AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap }
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config._
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function.QFunction
import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
import scala.language.reflectiveCalls
import scalaz.Scalaz._
-import scalaz._
/**
* Gentrap pipeline
@@ -62,13 +61,27 @@ class Gentrap(val root: Configurable) extends QScript
/** Expression measurement modes */
// see the enumeration below for valid modes
- var expMeasures: Set[ExpMeasures.Value] = config("expression_measures")
- .asStringList
- .map { makeExpMeasure }
- .toSet
+ var expMeasures: Set[ExpMeasures.Value] = {
+ if (config.contains("expression_measures"))
+ config("expression_measures")
+ .asStringList
+ .map { makeExpMeasure }
+ .toSet
+ else {
+ Logging.addError("'expression_measures' is missing in the config")
+ Set()
+ }
+ }
/** Strandedness modes */
- var strandProtocol: StrandProtocol.Value = makeStrandProtocol(config("strand_protocol").asString)
+ var strandProtocol: StrandProtocol.Value = {
+ if (config.contains("strand_protocol"))
+ makeStrandProtocol(config("strand_protocol").asString)
+ else {
+ Logging.addError("'strand_protocol' is missing in the config")
+ StrandProtocol.NonSpecific
+ }
+ }
/** GTF reference file */
var annotationGtf: Option[File] = config("annotation_gtf")
--
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