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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
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* 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.cli.FileSystemUtils._
import org.bdgenomics.adam.projections.AlignmentRecordField._
import org.bdgenomics.adam.projections.Projection
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.utils.cli._
import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
* 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"
def apply(cmdLine: Array[String]): BDGCommand = {
new Reads2Coverage(Args4j[Reads2CoverageArgs](cmdLine))
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 to", 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 = false
@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
@Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file")
var asSingleFile: Boolean = false
@Args4jOption(required = false, name = "-disable_fast_concat", usage = "Disables the parallel file concatenation engine.")
var disableFastConcat: Boolean = false
@Args4jOption(required = false, name = "-sort_lexicographically", usage = "Sort the reads lexicographically by contig name, instead of by index.")
var sortLexicographically: Boolean = false
class Reads2Coverage(protected val args: Reads2CoverageArgs) extends BDGSparkCommand[Reads2CoverageArgs] {
val companion: BDGCommandCompanion = Reads2Coverage
def run(sc: SparkContext): Unit = {
checkWriteablePath(args.outputPath, sc.hadoopConfiguration)
if (args.sortLexicographically) {
"-sort_lexicographically can only be provided when collapsing (-collapse).")
// 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")
// load reads
val readsRdd: AlignmentRecordDataset = sc.loadAlignments(args.inputPath)
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 {
val coverage = finalReads.toCoverage()
val maybeCollapsedCoverage = if (args.collapse) {
val sortedCoverage = if (args.sortLexicographically) {
} else {
} else {
asSingleFile = args.asSingleFile,
disableFastConcat = args.disableFastConcat)
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