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Fix compile error due to upstream 0.23.0-SNAPSHOT changes. #88

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Dec 25, 2017
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ class Freebayes(protected val args: FreebayesArgs) extends BDGSparkCommand[Freeb
val input: AlignmentRecordRDD = sc.loadAlignments(args.inputPath, stringency = stringency)

implicit val tFormatter = BAMInFormatter
implicit val uFormatter = new VCFOutFormatter
implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration)

val freebayesCommand = if (args.useDocker) {
Seq("docker",
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2 changes: 1 addition & 1 deletion cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ class SnpEff(protected val args: SnpEffArgs) extends BDGSparkCommand[SnpEffArgs]
val input: VariantContextRDD = sc.loadVcf(args.inputPath, stringency)

implicit val tFormatter = VCFInFormatter
implicit val uFormatter = new VCFOutFormatter
implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration)

val snpEffCommand = if (args.useDocker) {
Seq("docker",
Expand Down