Fixing reference for CRAM

Author: mwiewior

lib/hadoop-bam-8.0.1-SNAPSHOT.jar

@@ -111,14 +111,15 @@ trait BDGAlignFileReaderWriter [T <: BDGAlignInputFormat]{
             .hadoopConfiguration
             .unset("hadoopbam.bam.intervals")
 
-        logger.info(s"Setting BAM validation stringency to ${validationStringency.toString}")
+        logger.info(s"Setting BAM/CRAM validation stringency to ${validationStringency.toString}")
         spark
           .sparkContext
           .hadoopConfiguration
           .set(SAMHeaderReader.VALIDATION_STRINGENCY_PROPERTY, validationStringency.toString)
 
         refPath match {
           case Some(path) =>
+            logger.info(s"Using CRAM reference ${path}")
             spark
               .sparkContext
               .hadoopConfiguration

src/main/scala/org/biodatageeks/sequila/datasources/BAM/AlignmentRelation.scala

@@ -26,14 +26,10 @@ class Pileup(spark:SparkSession) {
         if (f == InputDataType.BAMInputDataType)
           new BAMTableReader[BAMBDGInputFormat](spark, tableName, sampleId, "bam", None)
         else if (f == InputDataType.CRAMInputDataType) {
-          val refPath = spark.sqlContext
-            .sparkContext
-            .hadoopConfiguration
-            .get(CRAMBDGInputFormat.REFERENCE_SOURCE_PATH_PROPERTY)
           new BAMTableReader[CRAMBDGInputFormat](spark, tableName, sampleId, "cram", Some(refPath))
         }
         else throw new Exception("Only BAM and CRAM file formats are supported.")
-      case None => throw new Exception("Wrong file extension - only BAM and CRAM file formats are supported.")
+      case None => throw new Exception("Empty file extension - BAM and CRAM file formats are supported.")
     }
     val (alignments, bounds) =
       tableReader