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refactored ReferenceFile to require SequenceDictionary
Added support for coverage calculation from alignment files [ADAM-1122] Remove Coverage and PairingRDD. Resolves #1122.
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adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Coverage.scala
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| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package org.bdgenomics.adam.cli | ||
|
|
||
| import org.apache.spark.SparkContext | ||
| import org.bdgenomics.adam.projections.AlignmentRecordField._ | ||
| import org.bdgenomics.adam.projections.Projection | ||
| import org.bdgenomics.adam.rdd.ADAMContext._ | ||
| import org.bdgenomics.adam.rdd.features.CoverageRDD | ||
| import org.bdgenomics.adam.rdd.read.{ AlignedReadRDD, AlignmentRecordRDD } | ||
| import org.bdgenomics.utils.cli._ | ||
| import org.kohsuke.args4j.{ Argument, Option => Args4jOption } | ||
|
|
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| /** | ||
| * Reads2Coverage (accessible as the command 'reads2coverage' through the CLI) takes two arguments, | ||
| * an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in | ||
| * the file. Optional arguments are only_negative_strands, only_positive_strands and collapse. | ||
| * only_negative_strands and only_positive_strands save coverage computed from only negative and positive strands, | ||
| * respectively. Collapse specifies whether saved coverage should merge neighboring coverage with the same counts | ||
| * to one record. | ||
| */ | ||
| object Reads2Coverage extends BDGCommandCompanion { | ||
| val commandName: String = "reads2coverage" | ||
| val commandDescription: String = "Calculate the coverage from a given ADAM file" | ||
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| def apply(cmdLine: Array[String]): BDGCommand = { | ||
| new Reads2Coverage(Args4j[Reads2CoverageArgs](cmdLine)) | ||
| } | ||
| } | ||
|
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| class Reads2CoverageArgs extends Args4jBase with ParquetArgs { | ||
| @Argument(required = true, metaVar = "INPUT", usage = "The reads file to use to calculate depths", index = 0) | ||
| var inputPath: String = null | ||
| @Argument(required = true, metaVar = "OUTPUT", usage = "Location to write the coverage data in ADAM/Parquet format", index = 1) | ||
| var outputPath: String = null | ||
| @Args4jOption(required = false, name = "-collapse", usage = "Collapses neighboring coverage records " + | ||
| "of equal counts into the same record") | ||
| var collapse: Boolean = true | ||
| @Args4jOption(required = false, name = "-only_negative_strands", usage = "Compute coverage for negative strands") | ||
| var onlyNegativeStrands: Boolean = false | ||
| @Args4jOption(required = false, name = "-only_positive_strands", usage = "Compute coverage for positive strands") | ||
| var onlyPositiveStrands: Boolean = false | ||
| } | ||
|
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| class Reads2Coverage(protected val args: Reads2CoverageArgs) extends BDGSparkCommand[Reads2CoverageArgs] { | ||
| val companion: BDGCommandCompanion = Reads2Coverage | ||
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| def run(sc: SparkContext): Unit = { | ||
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| val proj = Projection(contigName, start, end, cigar) | ||
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| // If saving strand specific coverage, require that only one direction is specified | ||
| require(!(args.onlyNegativeStrands && args.onlyPositiveStrands), | ||
| "Cannot compute coverage for both negative and positive strands separately") | ||
|
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| // load reads | ||
| val readsRdd: AlignmentRecordRDD = sc.loadAlignments(args.inputPath, projection = Some(proj)) | ||
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| val finalReads = if (args.onlyNegativeStrands && !args.onlyPositiveStrands) { | ||
| readsRdd.transform(rdd => rdd.filter(_.getReadNegativeStrand)) | ||
| } else if (!args.onlyNegativeStrands && args.onlyPositiveStrands) { | ||
| readsRdd.transform(rdd => rdd.filter(!_.getReadNegativeStrand)) | ||
| } else { | ||
| readsRdd | ||
| } | ||
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| finalReads.toCoverage(args.collapse) | ||
| .save(args.outputPath) | ||
| } | ||
| } | ||
|
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adam-cli/src/test/scala/org/bdgenomics/adam/cli/Reads2CoverageSuite.scala
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| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package org.bdgenomics.adam.cli | ||
|
|
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| import org.bdgenomics.adam.rdd.ADAMContext._ | ||
| import org.bdgenomics.adam.util.ADAMFunSuite | ||
| import org.bdgenomics.utils.cli.Args4j | ||
|
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| class Reads2CoverageSuite extends ADAMFunSuite { | ||
|
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| sparkTest("correctly calculates coverage from small sam file") { | ||
| val inputPath = copyResource("artificial.sam") | ||
| val outputPath = tmpFile("coverage.adam") | ||
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| val args: Array[String] = Array(inputPath, outputPath) | ||
| new Reads2Coverage(Args4j[Reads2CoverageArgs](args)).run(sc) | ||
| val coverage = sc.loadCoverage(outputPath) | ||
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| val pointCoverage = coverage.flatten.rdd.filter(_.start == 30).first | ||
| assert(pointCoverage.count == 5) | ||
| } | ||
| } | ||
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86
adam-core/src/main/scala/org/bdgenomics/adam/models/Coverage.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package org.bdgenomics.adam.models | ||
|
|
||
| import org.apache.spark.rdd.RDD | ||
| import org.bdgenomics.formats.avro.Feature | ||
|
|
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| /** | ||
| * Converts from avro Feature to Coverage. | ||
| */ | ||
| object Coverage { | ||
|
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| /** | ||
| * Creates Coverage from ReferenceRegion and coverage count in that ReferenceRegion. | ||
| * | ||
| * @param region ReferenceRegion in which Coverage spans | ||
| * @param count Coverage count for each base pair in region | ||
| * @return Coverage spanning the specified ReferenceRegion | ||
| */ | ||
| private[adam] def apply(region: ReferenceRegion, count: Double): Coverage = { | ||
| Coverage(region.referenceName, region.start, region.end, count) | ||
| } | ||
|
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| /** | ||
| * Creates Coverage from Feature, extracting region information and feature score for coverage. | ||
| * | ||
| * @param feature Feature to create coverage from | ||
| * @return Coverage spanning the specified feature | ||
| */ | ||
| private[adam] def apply(feature: Feature): Coverage = { | ||
| Coverage(feature.getContigName, feature.getStart, feature.getEnd, feature.getScore) | ||
| } | ||
|
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| /** | ||
| * Creates an RDD of Coverage from RDD of Features. | ||
| * | ||
| * @param rdd RDD of Features to extract Coverage from | ||
| * @return RDD of Coverage spanning all features in rdd | ||
| */ | ||
| private[adam] def apply(rdd: RDD[Feature]): RDD[Coverage] = { | ||
| rdd.map(f => Coverage(f)) | ||
| } | ||
| } | ||
|
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| /** | ||
| * Coverage record for CoverageRDD. | ||
| * Contains Region indexed by contig name, start and end, as well as count of coverage at | ||
| * each base pair in that region. | ||
| * | ||
| * @param contigName Specifies chromosomal location of coverage | ||
| * @param start Specifies start position of coverage | ||
| * @param end Specifies end position of coverage | ||
| * @param count Specifies count of coverage at location | ||
| */ | ||
| case class Coverage(contigName: String, start: Long, end: Long, count: Double) { | ||
|
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| /** | ||
| * Converts Coverage to Feature, setting Coverage count in the score attribute. | ||
| * | ||
| * @return Feature built from Coverage | ||
| */ | ||
| def toFeature: Feature = { | ||
| val fb = Feature.newBuilder() | ||
| fb.setContigName(contigName) | ||
| fb.setStart(start) | ||
| fb.setEnd(end) | ||
| fb.setScore(count) | ||
| fb.build() | ||
| } | ||
| } | ||
|
|
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