From f58c56c0a1852a590ecbdb600ade54d8e0b1614d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 25 Mar 2016 12:48:57 +0100
Subject: [PATCH] Added contig check
---
.../lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
index d0627bfbc..67e056a51 100644
--- a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
+++ b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
@@ -3,10 +3,12 @@ package nl.lumc.sasc.biopet.pipelines.gwastest
import java.io.File
import java.util
+import htsjdk.samtools.reference.FastaSequenceFile
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, BiopetQScript }
import nl.lumc.sasc.biopet.extensions.Cat
import nl.lumc.sasc.biopet.extensions.gatk.{ SelectVariants, CombineVariants }
import nl.lumc.sasc.biopet.extensions.tools.GensToVcf
+import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.broadinstitute.gatk.queue.QScript
@@ -45,8 +47,16 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
case _ => Nil
})
+ lazy val referenceDict = new FastaSequenceFile(referenceFasta(), true).getSequenceDictionary
+
+ override def dictRequired = true
+
/** Init for pipeline */
def init(): Unit = {
+ inputGens.foreach { g =>
+ if (referenceDict.getSequenceIndex(g.contig) == -1)
+ Logging.addError(s"Contig '${g.contig}' does not exist on reference: ${referenceFasta()}")
+ }
}
/** Pipeline itself */
--
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