org.apache.spark.sql.types.ShortType Scala Examples

The following examples show how to use org.apache.spark.sql.types.ShortType. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example.
Example 1
Source File: PileupTestBase.scala    From bdg-sequila   with Apache License 2.0 5 votes vote down vote up 
package org.biodatageeks.sequila.tests.pileup

import com.holdenkarau.spark.testing.{DataFrameSuiteBase, SharedSparkContext}
import org.apache.spark.sql.{Dataset, Row, SaveMode, SparkSession}
import org.apache.spark.sql.types.{IntegerType, ShortType, StringType, StructField, StructType}
import org.scalatest.{BeforeAndAfter, FunSuite}

class PileupTestBase extends FunSuite
  with DataFrameSuiteBase
  with BeforeAndAfter
  with SharedSparkContext{

  val sampleId = "NA12878.multichrom.md"
  val samResPath: String = getClass.getResource("/multichrom/mdbam/samtools.pileup").getPath
  val referencePath: String = getClass.getResource("/reference/Homo_sapiens_assembly18_chr1_chrM.small.fasta").getPath
  val bamPath: String = getClass.getResource(s"/multichrom/mdbam/${sampleId}.bam").getPath
  val cramPath : String = getClass.getResource(s"/multichrom/mdcram/${sampleId}.cram").getPath
  val tableName = "reads_bam"
  val tableNameCRAM = "reads_cram"

  val schema: StructType = StructType(
    List(
      StructField("contig", StringType, nullable = true),
      StructField("position", IntegerType, nullable = true),
      StructField("reference", StringType, nullable = true),
      StructField("coverage", ShortType, nullable = true),
      StructField("pileup", StringType, nullable = true),
      StructField("quality", StringType, nullable = true)
    )
  )
  before {
    System.setProperty("spark.kryo.registrator", "org.biodatageeks.sequila.pileup.serializers.CustomKryoRegistrator")
    spark
      .conf.set("spark.sql.shuffle.partitions",1) //FIXME: In order to get orderBy in Samtools tests working - related to exchange partitions stage
    spark.sql(s"DROP TABLE IF EXISTS $tableName")
    spark.sql(
      s"""
         |CREATE TABLE $tableName
         |USING org.biodatageeks.sequila.datasources.BAM.BAMDataSource
         |OPTIONS(path "$bamPath")
         |
      """.stripMargin)

    spark.sql(s"DROP TABLE IF EXISTS $tableNameCRAM")
    spark.sql(
      s"""
         |CREATE TABLE $tableNameCRAM
         |USING org.biodatageeks.sequila.datasources.BAM.CRAMDataSource
         |OPTIONS(path "$cramPath", refPath "$referencePath" )
         |
      """.stripMargin)

    val mapToString = (map: Map[Byte, Short]) => {
      if (map == null)
        "null"
      else
        map.map({
          case (k, v) => k.toChar -> v}).mkString.replace(" -> ", ":")
    }

    val byteToString = ((byte: Byte) => byte.toString)

    spark.udf.register("mapToString", mapToString)
    spark.udf.register("byteToString", byteToString)
  }

}