Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
4 changed files
with
379 additions
and
7 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
166 changes: 166 additions & 0 deletions
166
avocado-core/src/main/scala/org/bdgenomics/avocado/util/RewriteHets.scala
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,166 @@ | ||
| /** | ||
| * 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.avocado.util | ||
|
|
||
| import org.bdgenomics.adam.rdd.variant.GenotypeRDD | ||
| import org.bdgenomics.formats.avro.{ Genotype, GenotypeAllele } | ||
| import scala.collection.JavaConversions._ | ||
|
|
||
| private[avocado] trait RewriteHetsArgs extends Serializable { | ||
|
|
||
| /** | ||
| * The maximum allele fraction for the alternate allele in a het SNP call. | ||
| * | ||
| * Set to a negative value to omit. | ||
| */ | ||
| var maxHetSnpAltAllelicFraction: Float | ||
|
|
||
| /** | ||
| * The maximum allele fraction for the alternate allele in a het SNP call. | ||
| * | ||
| * Set to a negative value to omit. | ||
| */ | ||
| var maxHetIndelAltAllelicFraction: Float | ||
|
|
||
| /** | ||
| * If true, does not attempt to rewrite het SNPs. | ||
| */ | ||
| var disableHetSnpRewriting: Boolean | ||
|
|
||
| /** | ||
| * If true, does not attempt to rewrite het INDELs. | ||
| */ | ||
| var disableHetIndelRewriting: Boolean | ||
| } | ||
|
|
||
| /** | ||
| * Rewrites high allelic fraction het genotypes as homozygous alternate calls. | ||
| */ | ||
| object RewriteHets extends Serializable { | ||
|
|
||
| /** | ||
| * Identifies high allelic fraction het calls in an RDD of genotypes and | ||
| * rewrites them as homozygous alt calls. | ||
| * | ||
| * @param rdd The RDD of genotypes to filter. | ||
| * @param args The arguments to configure the rewriter. | ||
| * @return Returns a new RDD of genotypes. | ||
| */ | ||
| def apply(rdd: GenotypeRDD, | ||
| args: RewriteHetsArgs): GenotypeRDD = { | ||
|
|
||
| val maxSnpAllelicFraction = args.maxHetSnpAltAllelicFraction | ||
| val maxIndelAllelicFraction = args.maxHetIndelAltAllelicFraction | ||
| val rewriteHetSnps = !args.disableHetSnpRewriting | ||
| val rewriteHetIndels = !args.disableHetIndelRewriting | ||
|
|
||
| if (rewriteHetSnps || rewriteHetIndels) { | ||
| rdd.transform(gtRdd => gtRdd.map(processGenotype(_, | ||
| maxSnpAllelicFraction, | ||
| maxIndelAllelicFraction, | ||
| rewriteHetSnps, | ||
| rewriteHetIndels))) | ||
| } else { | ||
| rdd | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Examines a single genotype to see if it should be rewritten. | ||
| * | ||
| * @param gt The genotype to examine. | ||
| * @param maxSnpAllelicFraction The threshold for considering a het SNP call | ||
| * to be a miscalled homozygous SNP. | ||
| * @param maxIndelAllelicFraction The threshold for considering a het INDEL | ||
| * call to be a miscalled homozygous INDEL | ||
| * @param rewriteHetSnps If false, disables SNP checking. | ||
| * @param rewriteHetIndels If false, disables INDEL checking. | ||
| * @return Returns true if the genotype should be rewritten.. | ||
| */ | ||
| private[util] def shouldRewrite(gt: Genotype, | ||
| maxSnpAllelicFraction: Float, | ||
| maxIndelAllelicFraction: Float, | ||
| rewriteHetSnps: Boolean, | ||
| rewriteHetIndels: Boolean): Boolean = { | ||
| val isSnp = ((gt.getVariant.getReferenceAllele.length == 1) && | ||
| (gt.getVariant.getAlternateAllele.length == 1)) | ||
| val numAlts = gt.getAlleles.count(_ == GenotypeAllele.ALT) | ||
| val isHet = (numAlts != 0) && (numAlts != gt.getAlleles.length) | ||
|
|
||
| def checkAf(af: Float): Boolean = { | ||
| (Option(gt.getReadDepth), Option(gt.getAlternateReadDepth)) match { | ||
| case (Some(dp), Some(alt)) => (alt.toFloat / dp.toFloat) >= af | ||
| case _ => false | ||
| } | ||
| } | ||
|
|
||
| if (rewriteHetSnps && isSnp && isHet) { | ||
| checkAf(maxSnpAllelicFraction) | ||
| } else if (rewriteHetIndels && !isSnp && isHet) { | ||
| checkAf(maxIndelAllelicFraction) | ||
| } else { | ||
| false | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Rewrites a het genotype as a hom alt call. | ||
| * | ||
| * @param gt The genotype to rewrite. | ||
| * @return Returns the rewritten genotype. | ||
| */ | ||
| private[util] def rewriteGenotype(gt: Genotype): Genotype = { | ||
| val numAlleles = gt.getAlleles.length | ||
| val newAlleles = List.fill(numAlleles) { GenotypeAllele.ALT } | ||
|
|
||
| Genotype.newBuilder(gt) | ||
| .setGenotypeQuality(null) | ||
| .setAlleles(newAlleles) | ||
| .build | ||
| } | ||
|
|
||
| /** | ||
| * Processes a single genotype, and rewrites it if it appears to be a | ||
| * miscalled hom alt. | ||
| * | ||
| * @param gt The genotype to examine. | ||
| * @param maxSnpAllelicFraction The threshold for considering a het SNP call | ||
| * to be a miscalled homozygous SNP. | ||
| * @param maxIndelAllelicFraction The threshold for considering a het INDEL | ||
| * call to be a miscalled homozygous INDEL | ||
| * @param rewriteHetSnps If false, disables SNP checking. | ||
| * @param rewriteHetIndels If false, disables INDEL checking. | ||
| * @return Returns the rewritten genotype if the genotype should be rewritten, | ||
| * else returns the original genotype. | ||
| */ | ||
| private[util] def processGenotype(gt: Genotype, | ||
| maxSnpAllelicFraction: Float, | ||
| maxIndelAllelicFraction: Float, | ||
| rewriteHetSnps: Boolean, | ||
| rewriteHetIndels: Boolean): Genotype = { | ||
| if (shouldRewrite(gt, | ||
| maxSnpAllelicFraction, | ||
| maxIndelAllelicFraction, | ||
| rewriteHetSnps, | ||
| rewriteHetIndels)) { | ||
| rewriteGenotype(gt) | ||
| } else { | ||
| gt | ||
| } | ||
| } | ||
| } |
Oops, something went wrong.