Commit 9705d77d authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'fix-issue_248' into 'develop'

Fix issue #248

fix issue #248

See merge request !294
parents 72bf90bb bcfc47fd
......@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Gather, Output}
import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
......
......@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Gather, Output}
import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
......
......@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Gather, Output}
import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
......
......@@ -334,7 +334,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
override def beforeGraph(): Unit = {
super.beforeGraph()
if ((!gunzip && !bunzip2) && input.forall(_.getName.endsWith(".gz"))) {
logger.info("Fastq with .gz extension found, enabled --gunzip option")
logger.debug("Fastq with .gz extension found, enabled --gunzip option")
gunzip = true
}
}
......
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