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Personal tool to correct overlapping bases
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src/main/scala/com/fulcrumgenomics/personal/nhomer/CorrectOverlappingBases.scala
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| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2022 Fulcrum Genomics | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| * of this software and associated documentation files (the "Software"), to deal | ||
| * in the Software without restriction, including without limitation the rights | ||
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the Software is | ||
| * furnished to do so, subject to the following conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be included in | ||
| * all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| * THE SOFTWARE. | ||
| * | ||
| */ | ||
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| package com.fulcrumgenomics.personal.nhomer | ||
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| import com.fulcrumgenomics.FgBioDef.{FgBioEnum, PathToBam, FilePath, SafelyClosable, forloop} | ||
| import com.fulcrumgenomics.bam.Bams | ||
| import com.fulcrumgenomics.bam.api.{SamRecord, SamSource, SamWriter} | ||
| import com.fulcrumgenomics.cmdline.{ClpGroups, FgBioTool} | ||
| import com.fulcrumgenomics.commons.collection.ParIterator | ||
| import com.fulcrumgenomics.commons.util.LazyLogging | ||
| import com.fulcrumgenomics.commons.util.Threads.IterableThreadLocal | ||
| import com.fulcrumgenomics.sopt.{arg, clp} | ||
| import com.fulcrumgenomics.umi.SimpleConsensusCaller | ||
| import com.fulcrumgenomics.umi.VanillaUmiConsensusCallerOptions.{DefaultErrorRatePostUmi, DefaultErrorRatePreUmi} | ||
| import com.fulcrumgenomics.util.NumericTypes.PhredScore | ||
| import com.fulcrumgenomics.util.{Io, Metric, ProgressLogger} | ||
| import enumeratum.EnumEntry | ||
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| import scala.collection.immutable | ||
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| @clp(group = ClpGroups.SamOrBam, description= | ||
| """ | ||
| |Masks or corrects overlapping bases in FR read pairs. | ||
| """) | ||
| class CorrectOverlappingBases | ||
| ( @arg(flag='i', doc="Input SAM or BAM file of aligned reads in coordinate order.") val input: PathToBam, | ||
| @arg(flag='o', doc="Output SAM or BAM file.") val output: PathToBam, | ||
| @arg(flag='m', doc="Output metrics file.") val metrics: FilePath, | ||
| @arg(flag='g', doc="Maximum error rate of a gapless alignment before switching to a gapped alignment") val maxGaplessErrorRate: Double = 1.0, | ||
| @arg(flag='1', doc="The Phred-scaled error rate for an error prior to the UMIs being integrated.") val errorRatePreUmi: PhredScore = DefaultErrorRatePreUmi, | ||
| @arg(flag='2', doc="The Phred-scaled error rate for an error post the UMIs have been integrated.") val errorRatePostUmi: PhredScore = DefaultErrorRatePostUmi, | ||
| @arg(doc="Mask all corrected bases") val mask: Boolean = false, | ||
| @arg(doc="The number of threads to use while consensus calling.") val threads: Int = 1 | ||
| ) extends FgBioTool with LazyLogging { | ||
| Io.assertReadable(input) | ||
| Io.assertCanWriteFile(output) | ||
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| //private val matchScore: Int = 1 | ||
| //private val aligner: Aligner = Aligner(matchScore, -4, -6, -1, Mode.Global) | ||
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| private case class ThreadData(caller: SimpleConsensusCaller, templateMetric: CorrectOverlappingBasesMetric, basesMetric: CorrectOverlappingBasesMetric) | ||
| private object ThreadData { | ||
| def apply(): ThreadData = ThreadData( | ||
| caller = new SimpleConsensusCaller( | ||
| errorRatePreLabeling = errorRatePreUmi, | ||
| errorRatePostLabeling = errorRatePostUmi | ||
| ), | ||
| templateMetric = CorrectOverlappingBasesMetric(tpe=CountType.Templates), | ||
| basesMetric = CorrectOverlappingBasesMetric(tpe=CountType.Bases) | ||
| ) | ||
| } | ||
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| override def execute(): Unit = { | ||
| val source = SamSource(input) | ||
| val writer = SamWriter(output, source.header) | ||
| val progress = new ProgressLogger(logger) | ||
| val templateIterator = Bams.templateIterator(source) | ||
| val threadData = new IterableThreadLocal(() => ThreadData()) | ||
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| ParIterator(templateIterator, threads=threads) | ||
| .map { template => | ||
| val threadDatum = threadData.get() | ||
| threadDatum.synchronized { | ||
| // update metrics | ||
| threadDatum.templateMetric.total += 1 | ||
| threadDatum.basesMetric.total += template.primaryReads.map(_.length).sum | ||
| // corrects | ||
| (template.r1, template.r2) match { | ||
| case (Some(r1), Some(r2)) if r1.mapped && r2.mapped && r1.matesOverlap.contains(true) && r1.isFrPair => | ||
| if (r1.positiveStrand) correct(r1, r2, threadDatum) else correct(r2, r1, threadDatum) | ||
| case _ => () | ||
| } | ||
| } | ||
| template.allReads.foreach(progress.record) | ||
| template | ||
| }.toAsync(ParIterator.DefaultChunkSize * 8).foreach { template => | ||
| writer ++= template.allReads | ||
| } | ||
| progress.logLast() | ||
| source.safelyClose() | ||
| writer.close() | ||
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| val templatesMetric = CorrectOverlappingBasesMetric(tpe=CountType.Templates) | ||
| val basesMetric = CorrectOverlappingBasesMetric(tpe=CountType.Bases) | ||
| threadData.foreach { datum => | ||
| templatesMetric += datum.templateMetric | ||
| basesMetric += datum.basesMetric | ||
| } | ||
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| Metric.write(metrics, templatesMetric, basesMetric) | ||
| } | ||
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| private def positiveOrElse(readPos: Int, default: Int): Int = if (readPos <= 0) default else readPos | ||
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| private def correct(r1: SamRecord, r2: SamRecord, | ||
| data: ThreadData): Unit = { | ||
| val r1OldBases = r1.basesString | ||
| val r2OldBases = r2.basesString | ||
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| // TODO: adjust based on leading/trailing soft-clipping that may make lengths differ between extracted sequence | ||
| // Get the read sequences that overlap in R1 and R2 respectively, 0-based exclusive | ||
| val r1From = Math.max(0, r1.readPosAtRefPos(r2.start, returnLastBaseIfDeleted=false).getOrElse(0) - 1) | ||
| val r1Until = positiveOrElse(r1.readPosAtRefPos(r2.end, returnLastBaseIfDeleted=false).getOrElse(0), r1.length) | ||
| val r2From = Math.max(0, r2.readPosAtRefPos(r1.start, returnLastBaseIfDeleted=false).getOrElse(0) - 1) | ||
| val r2Until = positiveOrElse(r2.readPosAtRefPos(r1.end, returnLastBaseIfDeleted=false).getOrElse(0), r2.length) | ||
| val r1Sub = r1OldBases.slice(from=r1From, until=r1Until) | ||
| val r2Sub = r2OldBases.slice(from=r2From, until=r2Until) | ||
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| data.templateMetric.overlapping += 1 | ||
| data.basesMetric.overlapping += r1.length + r2.length | ||
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| // For now, ignore indels, but it would be hard to handle them. | ||
| require(r1Sub.nonEmpty || r2Sub.nonEmpty) | ||
| if (r1Sub.length != r2Sub.length) { | ||
| data.templateMetric.mismatch_length += 1 | ||
| data.basesMetric.mismatch_length += r1Sub.length + r2Sub.length | ||
| } else if (this.maxGaplessErrorRate < errorRate(r1Sub, r2Sub)) { | ||
| data.templateMetric.error_rate_too_high += 1 | ||
| data.basesMetric.error_rate_too_high += r1Sub.length + r2Sub.length | ||
| } else { | ||
| val r1OldQuals = r1.qualsString | ||
| val r2OldQuals = r2.qualsString | ||
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| // get the consensus | ||
| val result = data.caller.callBasesAndQualities( | ||
| sequences = Seq(r1Sub, r2Sub), | ||
| qualities = Seq(r1.quals.slice(from=r1From, until=r1Until), r2.quals.slice(from=r2From, until=r2Until)) | ||
| ) | ||
| val (bases, quals) = result match { | ||
| case (_, None) => throw new IllegalStateException("Bug: passed in two sequences, should have qualities returned") | ||
| case (b, Some(q)) => (b, q) | ||
| } | ||
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| // replace the bases and qualities | ||
| r1.bases = r1OldBases.take(r1From) + bases + r1OldBases.drop(r1Until) | ||
| r1.quals = r1OldQuals.take(r1From) + quals + r1OldQuals.drop(r1Until) | ||
| r2.bases = r2OldBases.take(r2From) + bases + r2OldBases.drop(r2Until) | ||
| r2.quals = r2OldQuals.take(r2From) + quals + r2OldQuals.drop(r2Until) | ||
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| val maybeMaskedBases: String = if (!mask) bases else { | ||
| val builder = new StringBuilder(r1Sub.length) | ||
| forloop(from = 0, until = r1Sub.length) { i => | ||
| if (bases(i) != r1Sub(i) || bases(i) != r2Sub(i)) builder.append('N') | ||
| else builder.append(bases(i)) | ||
| } | ||
| builder.toString | ||
| } | ||
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| // update metrics | ||
| var basesCorrected = 0 | ||
| var basesMasked = 0 | ||
| forloop(from = 0, until = r1Sub.length) { i => | ||
| if (maybeMaskedBases(i) == 'N') basesMasked += 2 | ||
| else { | ||
| if (maybeMaskedBases(i) != r1Sub(i)) basesCorrected += 1 | ||
| if (maybeMaskedBases(i) != r2Sub(i)) basesCorrected += 1 | ||
| } | ||
| } | ||
| if (basesMasked > 0) { | ||
| data.templateMetric.masked += 1 | ||
| data.basesMetric.masked += basesMasked | ||
| } | ||
| if (basesCorrected > 0) { | ||
| data.templateMetric.corrected += 1 | ||
| data.basesMetric.corrected += basesCorrected | ||
| } | ||
| data.templateMetric.examined += 1 | ||
| data.basesMetric.examined += r1Sub.length + r2Sub.length | ||
| } | ||
| } | ||
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| private def errorRate(query: String, target: String): Double = { | ||
| require(query.length == target.length) | ||
| require(query.nonEmpty) | ||
| var errors = 0 | ||
| forloop (from = 0, until = query.length) { i => | ||
| if (query(i) != target(i)) errors += 1 | ||
| } | ||
| errors / query.length | ||
| } | ||
| } | ||
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| case class CorrectOverlappingBasesMetric | ||
| ( | ||
| tpe: CountType, | ||
| var total: Long = 0, | ||
| var overlapping: Long = 0, | ||
| var mismatch_length: Long = 0, | ||
| var error_rate_too_high: Long = 0, | ||
| var examined: Long = 0, | ||
| var masked: Long = 0, | ||
| var corrected: Long = 0, | ||
| ) extends Metric { | ||
| def +=(other: CorrectOverlappingBasesMetric): CorrectOverlappingBasesMetric = { | ||
| require(this.tpe == other.tpe) | ||
| this.total += other.total | ||
| this.overlapping += other.overlapping | ||
| this.mismatch_length += other.mismatch_length | ||
| this.error_rate_too_high += other.error_rate_too_high | ||
| this.examined += other.examined | ||
| this.masked += other.masked | ||
| this.corrected += other.corrected | ||
| this | ||
| } | ||
| } | ||
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| sealed trait CountType extends EnumEntry | ||
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| object CountType extends FgBioEnum[CountType] { | ||
| case object Templates extends CountType | ||
| case object Bases extends CountType | ||
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| override def values: immutable.IndexedSeq[CountType] = findValues | ||
| } |
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