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added contigName Hive style partitioning to AlignmentRecordRDD #17

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added contigName Hive style partitioning to AlignmentRecordRDD #17

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11 changes: 9 additions & 2 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
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Expand Up @@ -190,8 +190,15 @@ case class DatasetBoundAlignmentRecordRDD private[rdd] (
compressCodec: CompressionCodecName = CompressionCodecName.GZIP,
disableDictionaryEncoding: Boolean = false) {
log.warn("Saving directly as Parquet from SQL. Options other than compression codec are ignored.")
dataset.toDF()
.write
import org.apache.spark.sql.functions._
val posBinSize: Int = 10000
val df = dataset.toDF()

// to be added when bdg-formats avro is updated with posBin field
// df.withColumn("posBin", floor(df("start") / posBinSize))
df.write
//.partitionBy("contigName", "posBin") // to be added when avro updated with posBin
.partitionBy("contigName")
.format("parquet")
.option("spark.sql.parquet.compression.codec", compressCodec.toString.toLowerCase())
.save(filePath)
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