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added predicate option to loadCoverage #1156

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added predicate option to loadCoverage #1156

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17 changes: 14 additions & 3 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -955,16 +955,27 @@ class ADAMContext private (@transient val sc: SparkContext) extends Serializable
FragmentRDD.fromRdd(records.map(fastqRecordConverter.convertFragment))
}

/**
* Loads file of Features to a CoverageRDD.
* Coverage is stored in the score attribute of Feature.
*
* @param filePath File path to load coverage from.
* @return CoverageRDD containing an RDD of Coverage
*/
def loadCoverage(filePath: String): CoverageRDD = loadFeatures(filePath).toCoverage

/**
* Loads Parquet file of Features to a CoverageRDD.
* Coverage is stored in the score attribute of Feature.
*
* @param filePath File path to load coverage from
* @param filePath File path to load coverage from.
* @param predicate An optional predicate to push down into the file.
* @return CoverageRDD containing an RDD of Coverage
*/
def loadCoverage(filePath: String): CoverageRDD = {
def loadParquetCoverage(filePath: String,
predicate: Option[FilterPredicate] = None): CoverageRDD = {
val proj = Projection(FeatureField.contigName, FeatureField.start, FeatureField.end, FeatureField.score)
loadFeatures(filePath, projection = Some(proj)).toCoverage
loadParquetFeatures(filePath, predicate = predicate, projection = Some(proj)).toCoverage
}

/**
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25 changes: 24 additions & 1 deletion adam-core/src/test/scala/org/bdgenomics/adam/rdd/features/CoverageRDDSuite.scala
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Expand Up @@ -17,7 +17,13 @@
*/
package org.bdgenomics.adam.rdd.features

import org.bdgenomics.adam.models.{ Coverage, SequenceDictionary, SequenceRecord }
import org.apache.parquet.filter2.dsl.Dsl._
import org.bdgenomics.adam.models.{
ReferenceRegion,
Coverage,
SequenceDictionary,
SequenceRecord
}
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.util.ADAMFunSuite
import org.bdgenomics.formats.avro.Feature
Expand Down Expand Up @@ -54,6 +60,23 @@ class CoverageRDDSuite extends ADAMFunSuite {
assert(coverage.rdd.count == 3)
}

sparkTest("correctly filters coverage with predicate") {
val f1 = Feature.newBuilder().setContigName("chr1").setStart(1).setEnd(10).setScore(3.0).build()
val f2 = Feature.newBuilder().setContigName("chr1").setStart(15).setEnd(20).setScore(2.0).build()
val f3 = Feature.newBuilder().setContigName("chr2").setStart(15).setEnd(20).setScore(2.0).build()

val featureRDD: FeatureRDD = FeatureRDD(sc.parallelize(Seq(f1, f2, f3)))
val coverageRDD: CoverageRDD = featureRDD.toCoverage

val outputFile = tmpLocation(".adam")
coverageRDD.save(outputFile, false)

val region = ReferenceRegion("chr1", 1, 9)
val predicate = ((LongColumn("end") >= region.start) && (LongColumn("start") <= region.end) && (BinaryColumn("contigName") === region.referenceName))
val coverage = sc.loadParquetCoverage(outputFile, Some(predicate))
assert(coverage.rdd.count == 1)
}

sparkTest("correctly flatmaps coverage without aggregated bins") {
val f1 = Feature.newBuilder().setContigName("chr1").setStart(1).setEnd(5).setScore(1.0).build()
val f2 = Feature.newBuilder().setContigName("chr1").setStart(5).setEnd(7).setScore(3.0).build()
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