Merge pull request #259 from Ferlab-Ste-Justine/fix/clin-2536

fix: CLIN-2536 glow register for vcf loading and some coloumns name changes
Ferlab-Ste-Justine · Jan 10, 2025 · 0a41e24 · 0a41e24
2 parents a508dc3 + 12db289
commit 0a41e24
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/datalake-spark3/src/main/scala/bio/ferlab/datalake/spark3/implicits/GenomicImplicits.scala b/datalake-spark3/src/main/scala/bio/ferlab/datalake/spark3/implicits/GenomicImplicits.scala
@@ -812,7 +812,8 @@ object GenomicImplicits {
   def vcf(input: String, referenceGenomePath: Option[String], optional: Boolean, split: Boolean)(implicit spark: SparkSession): DataFrame = {
     try {
       val inputs = input.split(",")
-      val df = spark.read
+      val sess = Glow.register(spark)
+      val df = sess.read
         .format("vcf")
         .option("flattenInfoFields", "true")
         .load(inputs: _*)