Merge 5c29dde into 67890b8

adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala

@@ -131,6 +131,8 @@ class TransformAlignmentsArgs extends Args4jBase with ADAMSaveAnyArgs with Parqu
   var storageLevel: String = "MEMORY_ONLY"
   @Args4jOption(required = false, name = "-disable_pg", usage = "Disable writing a new @PG line.")
   var disableProcessingStep = false
+  @Args4jOption(required = false, name = "-save_as_dataset", usage = "EXPERIMENTAL: Save as a Parquet format Spark-SQL dataset")
+  var saveAsDataset = false
 
   var command: String = null
 }
@@ -562,8 +564,12 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
       mergedSd
     }
 
-    outputRdd.save(args,
-      isSorted = args.sortReads || args.sortLexicographically)
+    if (args.saveAsDataset) {
+      outputRdd.saveAsPartitionedParquet(args.outputPath)
+    } else {
+      outputRdd.save(args,
+        isSorted = args.sortReads || args.sortLexicographically)
+    }
   }
 
   private def createKnownSnpsTable(sc: SparkContext): SnpTable = {

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

@@ -1866,6 +1866,35 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     }
   }
 
+  /**
+   * Load a path name with range binned partitioned Parquet + Avro format into an AlignmentRecordRDD.
+   *
+   * @note The sequence dictionary is read from an Avro file stored at
+   *   pathName/_seqdict.avro and the record group dictionary is read from an
+   *   Avro file stored at pathName/_rgdict.avro. These files are pure Avro,
+   *   not Parquet + Avro.
+   *
+   * @param pathName The path name to load alignment records from.
+   *   Globs/directories are supported.
+   * @param regions Optional list of genomic regions to load.
+   * @return Returns an AlignmentRecordRDD.
+   */
+  def loadPartitionedParquetAlignments(pathName: String,
+                                       regions: Iterable[ReferenceRegion] = Iterable.empty): AlignmentRecordRDD = {
+
+    val partitionedBinSize = getPartitionedBinSize(pathName)
+    val reads = loadParquetAlignments(pathName)
+
+    val datasetBoundAlignmentRecordRDD = if (regions.nonEmpty) {
+      DatasetBoundAlignmentRecordRDD(reads.dataset, reads.sequences, reads.recordGroups, reads.processingSteps, Some(partitionedBinSize))
+        .filterByOverlappingRegions(regions)
+    } else {
+      DatasetBoundAlignmentRecordRDD(reads.dataset, reads.sequences, reads.recordGroups, reads.processingSteps)
+    }
+
+    datasetBoundAlignmentRecordRDD
+  }
+
   /**
    * Load unaligned alignment records from interleaved FASTQ into an AlignmentRecordRDD.
    *
@@ -2249,6 +2278,30 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     }
   }
 
+  /**
+   * Load a path name with range binned partitioned Parquet + Avro format into GenotypeRDD
+   *
+   * @param pathName The path name to load alignment records from.
+   *   Globs/directories are supported.
+   * @param regions Optional list of genomic regions to load.
+   * @return Returns a GenotypeRDD.
+   */
+  def loadPartitionedParquetGenotypes(pathName: String,
+                                      regions: Iterable[ReferenceRegion] = Iterable.empty): GenotypeRDD = {
+
+    val partitionedBinSize = getPartitionedBinSize(pathName)
+    val genotypes = loadParquetGenotypes(pathName)
+
+    val datasetBoundGenotypeRDD = if (regions.nonEmpty) {
+      DatasetBoundGenotypeRDD(genotypes.dataset, genotypes.sequences, genotypes.samples, genotypes.headerLines, Some(partitionedBinSize))
+        .filterByOverlappingRegions(regions)
+    } else {
+      DatasetBoundGenotypeRDD(genotypes.dataset, genotypes.sequences, genotypes.samples, genotypes.headerLines, Some(partitionedBinSize))
+    }
+
+    datasetBoundGenotypeRDD
+  }
+
   /**
    * Load a path name in Parquet + Avro format into a VariantRDD.
    *
@@ -2282,6 +2335,30 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     }
   }
 
+  /**
+   * Load a path name with range binned partitioned Parquet + Avro format into an VariantRDD.
+   *
+   * @param pathName The path name to load alignment records from.
+   *   Globs/directories are supported.
+   * @param regions Optional list of genomic regions to load.
+   * @return Returns a VariantRDD
+   */
+  def loadPartitionedParquetVariants(pathName: String,
+                                     regions: Iterable[ReferenceRegion] = Iterable.empty): VariantRDD = {
+
+    val partitionedBinSize = getPartitionedBinSize(pathName)
+    val variants = loadParquetVariants(pathName)
+
+    val datasetBoundVariantRDD = if (regions.nonEmpty) {
+      DatasetBoundVariantRDD(variants.dataset, variants.sequences, variants.headerLines, Some(partitionedBinSize))
+        .filterByOverlappingRegions(regions)
+    } else {
+      DatasetBoundVariantRDD(variants.dataset, variants.sequences, variants.headerLines, Some(partitionedBinSize))
+    }
+
+    datasetBoundVariantRDD
+  }
+
   /**
    * Load nucleotide contig fragments from FASTA into a NucleotideContigFragmentRDD.
    *
@@ -2598,6 +2675,30 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     }
   }
 
+  /**
+   * Load a path name with range binned partitioned Parquet + Avro format into a FeatureRDD.
+   *
+   * @param pathName The path name to load alignment records from.
+   *   Globs/directories are supported.
+   * @param regions Optional list of genomic regions to load.
+   * @return Returns a FeatureRDD.
+   */
+  def loadPartitionedParquetFeatures(pathName: String,
+                                     regions: Iterable[ReferenceRegion] = Iterable.empty): FeatureRDD = {
+
+    val partitionedBinSize = getPartitionedBinSize(pathName)
+    val features = loadParquetFeatures(pathName)
+
+    val datasetBoundFeatureRDD = if (regions.nonEmpty) {
+      DatasetBoundFeatureRDD(features.dataset, features.sequences, Some(partitionedBinSize))
+        .filterByOverlappingRegions(regions)
+    } else {
+      DatasetBoundFeatureRDD(features.dataset, features.sequences, Some(partitionedBinSize))
+    }
+
+    datasetBoundFeatureRDD
+  }
+
   /**
    * Load a path name in Parquet + Avro format into a NucleotideContigFragmentRDD.
    *
@@ -2630,6 +2731,30 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     }
   }
 
+  /**
+   * Load a path name with range binned partitioned Parquet + Avro format into a NucleotideContigFragmentRDD.
+   *
+   * @param pathName The path name to load alignment records from.
+   *   Globs/directories are supported.
+   * @param regions Optional list of genomic regions to load.
+   * @return Returns a NucleotideContigFragmentRDD
+   */
+  def loadPartitionedParquetContigFragments(pathName: String,
+                                            regions: Iterable[ReferenceRegion] = Iterable.empty): NucleotideContigFragmentRDD = {
+
+    val partitionedBinSize = getPartitionedBinSize(pathName)
+    val contigs = loadParquetContigFragments(pathName)
+
+    val datasetBoundNucleotideContigFragmentRDD = if (regions.nonEmpty) {
+      DatasetBoundNucleotideContigFragmentRDD(contigs.dataset, contigs.sequences, Some(partitionedBinSize))
+        .filterByOverlappingRegions(regions)
+    } else {
+      DatasetBoundNucleotideContigFragmentRDD(contigs.dataset, contigs.sequences, Some(partitionedBinSize))
+    }
+
+    datasetBoundNucleotideContigFragmentRDD
+  }
+
   /**
    * Load a path name in Parquet + Avro format into a FragmentRDD.
    *
@@ -3051,4 +3176,27 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
       loadParquetFragments(pathName, optPredicate = optPredicate, optProjection = optProjection)
     }
   }
+
+  /**
+   * Return true if the specified path of Parquet + Avro files is partitioned.
+   *
+   * @param pathName Path in which to look for partitioned flag.
+   * @return Return true if the specified path of Parquet + Avro files is partitioned.
+   *
+   * If a glob is used, all directories within the blog must be partitioned, and must have been saved
+   * using the same partitioned bin size.  Behavior is undefined if this requirement is not met.
+   */
+  def getPartitionedBinSize(pathName: String): Int = {
+
+    val partitionSize = try {
+      val f = getFsAndFilesWithFilter(pathName, new FileFilter("_isPartitionedByStartPos")).head
+      f.getFileSystem(sc.hadoopConfiguration).open(f).readInt()
+    } catch {
+      case e: FileNotFoundException => {
+        throw new FileNotFoundException("Input Parquet files (%s) are not partitioned.".format(pathName))
+      }
+    }
+    partitionSize
+  }
+
 }

adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala

@@ -20,14 +20,15 @@ package org.bdgenomics.adam.rdd
 import java.nio.file.Paths
 import htsjdk.samtools.ValidationStringency
 import org.apache.avro.generic.IndexedRecord
-import org.apache.hadoop.fs.Path
+import org.apache.hadoop.fs.{ FSDataOutputStream, FileSystem, Path }
 import org.apache.parquet.hadoop.metadata.CompressionCodecName
 import org.apache.spark.SparkFiles
 import org.apache.spark.api.java.JavaRDD
 import org.apache.spark.api.java.function.{ Function => JFunction, Function2 }
 import org.apache.spark.broadcast.Broadcast
 import org.apache.spark.rdd.RDD
 import org.apache.spark.sql.{ DataFrame, Dataset, SQLContext }
+import org.apache.spark.sql.functions._
 import org.apache.spark.storage.StorageLevel
 import org.bdgenomics.adam.instrumentation.Timers._
 import org.bdgenomics.adam.models.{
@@ -54,6 +55,7 @@ import scala.collection.JavaConversions._
 import scala.math.min
 import scala.reflect.ClassTag
 import scala.reflect.runtime.universe.TypeTag
+import scala.util.Try
 
 private[rdd] class JavaSaveArgs(var outputPath: String,
                                 var blockSize: Int = 128 * 1024 * 1024,
@@ -2324,6 +2326,19 @@ trait GenomicDataset[T, U <: Product, V <: GenomicDataset[T, U, V]] extends Geno
         convFn.call(v, dsX)
       })
   }
+
+  /**
+   * Filters and replaces the underlying dataset based on overlap with any of a Seq of ReferenceRegions.
+   *
+   * @param querys ReferencesRegions to filter against
+   * @param optPartitionedLookBackNum Optional number of parquet position bins to look back to find start of a
+   *                                  ReferenceRegion, defaults to 1
+   * @return Returns a new DatasetBoundGenomicRDD with ReferenceRegions filter applied.
+   */
+  def filterDatasetByOverlappingRegions(querys: Iterable[ReferenceRegion],
+                                        optPartitionedLookBackNum: Option[Int] = Some(1)): V = {
+    filterByOverlappingRegions(querys)
+  }
 }
 
 trait GenomicRDDWithLineage[T, U <: GenomicRDDWithLineage[T, U]] extends GenomicRDD[T, U] {
@@ -2531,6 +2546,23 @@ abstract class AvroGenomicRDD[T <% IndexedRecord: Manifest, U <: Product, V <: A
     saveSequences(filePath)
   }
 
+  protected def referenceRegionsToDatasetQueryString(regions: Iterable[ReferenceRegion], partitionSize: Int = 1000000, partitionedLookBackNum: Int = 1): String = {
+
+    //test if this dataset is bound to Partitioned Parquet having field positionBin
+    if (Try(dataset("positionBin")).isSuccess) {
+      regions.map(r => "(contigName=" + "\'" + r.referenceName +
+        "\' and positionBin >= \'" + ((scala.math.floor(r.start / partitionSize).toInt) - partitionedLookBackNum) +
+        "\' and positionBin < \'" + (scala.math.floor(r.end / partitionSize).toInt + 1) +
+        "\' and (end > " + r.start + " and start < " + r.end + "))")
+        .mkString(" or ")
+    } else { // if no positionBin field is found then construct query without bin optimization
+      regions.map(r => "(contigName=" + "\'" + r.referenceName +
+        "\' and (end > " + r.start + " and start < " + r.end + "))")
+        .mkString(" or ")
+    }
+
+  }
+
   /**
    * Saves RDD as a directory of Parquet files.
    *
@@ -2606,4 +2638,41 @@ abstract class AvroGenomicRDD[T <% IndexedRecord: Manifest, U <: Product, V <: A
   def saveAsParquet(filePath: java.lang.String) {
     saveAsParquet(new JavaSaveArgs(filePath))
   }
+
+  /**
+   * Saves this RDD to disk in range binned partitioned Parquet + Avro format
+   *
+   * @param filePath Path to save the file at.
+   */
+  private def writePartitionedParquetFlag(filePath: String, partitionSize: Int): Unit = {
+    val path = new Path(filePath, "_isPartitionedByStartPos")
+    val fs: FileSystem = path.getFileSystem(rdd.context.hadoopConfiguration)
+    val f = fs.create(path)
+    f.writeInt(partitionSize)
+    f.close()
+  }
+
+  /**
+   *  Saves this RDD to disk in range binned partitioned Parquet + Avro format
+   *
+   * @param filePath Path to save the file at.
+   * @param compressCodec Name of the compression codec to use.
+   * @param partitionSize size of partitions used when writing parquet, in base pairs.  Defaults to 1000000.
+   */
+  def saveAsPartitionedParquet(filePath: String,
+                               compressCodec: CompressionCodecName = CompressionCodecName.GZIP,
+                               partitionSize: Int = 1000000) {
+    log.warn("Saving directly as Hive-partitioned Parquet from SQL. " +
+      "Options other than compression codec are ignored.")
+    val df = toDF()
+    df.withColumn("positionBin", floor(df("start") / partitionSize))
+      .write
+      .partitionBy("contigName", "positionBin")
+      .format("parquet")
+      .option("spark.sql.parquet.compression.codec", compressCodec.toString.toLowerCase())
+      .save(filePath)
+    writePartitionedParquetFlag(filePath, partitionSize)
+    saveMetadata(filePath)
+  }
+
 }

adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDD.scala

@@ -137,9 +137,9 @@ case class ParquetUnboundNucleotideContigFragmentRDD private[rdd] (
 
 case class DatasetBoundNucleotideContigFragmentRDD private[rdd] (
   dataset: Dataset[NucleotideContigFragmentProduct],
-  sequences: SequenceDictionary) extends NucleotideContigFragmentRDD
+  sequences: SequenceDictionary,
+  partitionedBinSize: Option[Int] = None) extends NucleotideContigFragmentRDD
     with DatasetBoundGenomicDataset[NucleotideContigFragment, NucleotideContigFragmentProduct, NucleotideContigFragmentRDD] {
-
   lazy val rdd: RDD[NucleotideContigFragment] = dataset.rdd.map(_.toAvro)
 
   protected lazy val optPartitionMap = None
@@ -162,6 +162,24 @@ case class DatasetBoundNucleotideContigFragmentRDD private[rdd] (
     newSequences: SequenceDictionary): NucleotideContigFragmentRDD = {
     copy(sequences = newSequences)
   }
+
+  override def transformDataset(tFn: Dataset[NucleotideContigFragmentProduct] => Dataset[NucleotideContigFragmentProduct]): NucleotideContigFragmentRDD = {
+    copy(dataset = tFn(dataset))
+  }
+
+  /**
+   * Filters and replaces the underlying dataset based on overlap with any of a Seq of ReferenceRegions.
+   *
+   * @param querys ReferencesRegions to filter against
+   * @param optPartitionedLookBackNum Optional number of parquet position bins to look back to find start of a
+   *                                  ReferenceRegion, defaults to 1
+   * @return Returns a new DatasetBoundNucleotideContigFragmentRDD with ReferenceRegions filter applied.
+   */
+  override def filterDatasetByOverlappingRegions(querys: Iterable[ReferenceRegion],
+                                                 optPartitionedLookBackNum: Option[Int] = Some(1)): NucleotideContigFragmentRDD = {
+    transformDataset((d: Dataset[org.bdgenomics.adam.sql.NucleotideContigFragment]) =>
+      d.filter(referenceRegionsToDatasetQueryString(querys, partitionedBinSize.get, optPartitionedLookBackNum.get)))
+  }
 }
 
 /**

adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala

@@ -276,7 +276,8 @@ case class ParquetUnboundFeatureRDD private[rdd] (
 
 case class DatasetBoundFeatureRDD private[rdd] (
   dataset: Dataset[FeatureProduct],
-  sequences: SequenceDictionary) extends FeatureRDD
+  sequences: SequenceDictionary,
+  partitionedBinSize: Option[Int] = None) extends FeatureRDD
     with DatasetBoundGenomicDataset[Feature, FeatureProduct, FeatureRDD] {
 
   lazy val rdd = dataset.rdd.map(_.toAvro)
@@ -312,6 +313,22 @@ case class DatasetBoundFeatureRDD private[rdd] (
       .withColumnRenamed("score", "count")
       .as[Coverage], sequences)
   }
+
+  /**
+   * Filters and replaces the underlying dataset based on overlap with any of a Seq of ReferenceRegions.
+   *
+   * @param querys ReferencesRegions to filter against
+   * @param optPartitionedLookBackNum Optional number of parquet position bins to look back to find start of a
+   *                                  ReferenceRegion, defaults to 1
+   * @return Returns a new DatasetBoundFeatureRDD with ReferenceRegions filter applied.
+   */
+  override def filterDatasetByOverlappingRegions(querys: Iterable[ReferenceRegion],
+                                                 optPartitionedLookBackNum: Option[Int] = Some(1)): FeatureRDD = {
+
+    transformDataset((d: Dataset[org.bdgenomics.adam.sql.Feature]) =>
+      d.filter(referenceRegionsToDatasetQueryString(querys, partitionedBinSize.get, optPartitionedLookBackNum.get)))
+  }
+
 }
 
 case class RDDBoundFeatureRDD private[rdd] (