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[AVOCADO-200] Feed assembled variants to INDEL realigner.
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363. * Adds a ConsensusRealigner that uses the main Realigner to realign reads, which are then fed into the variant discovery engine with loose filters. Any INDEL variants that are discovered are then fed in to ADAM's INDEL realignment engine as known INDELs. * Uses this realignment mode in the BiallelicGenotyperSuite to clean up a previously failing test. * Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
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avocado-core/src/main/scala/org/bdgenomics/avocado/realigner/ConsensusRealigner.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.avocado.realigner | ||
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| import org.bdgenomics.adam.algorithms.consensus.ConsensusGenerator | ||
| import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD | ||
| import org.bdgenomics.adam.rdd.variant.VariantRDD | ||
| import org.bdgenomics.avocado.genotyping.DiscoverVariants | ||
| import org.bdgenomics.formats.avro.Variant | ||
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| object ConsensusRealigner { | ||
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| /** | ||
| * Realigns a set of reads against the reference genome. | ||
| * | ||
| * @param reads Reads to realign. | ||
| * @param kmerLength The length k of the k-mers. | ||
| * @return Returns the realigned reads. | ||
| */ | ||
| def realign(reads: AlignmentRecordRDD, | ||
| kmerLength: Int): AlignmentRecordRDD = { | ||
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| // use the realigner to make a first pass over the reads | ||
| val realignedReads = Realigner.realign(reads, kmerLength) | ||
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| // from here, we'll discover any potential variants | ||
| val variants = filterIndels(DiscoverVariants(realignedReads)) | ||
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| // we'll pass these discovered variants to ADAM's indel realigner | ||
| reads.realignIndels(ConsensusGenerator.fromKnownIndels(variants)) | ||
| } | ||
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| /** | ||
| * @param v The variant to filter. | ||
| * @return Returns false if the variant is a SNV/MNV. | ||
| */ | ||
| private[realigner] def discardSnvs(v: Variant): Boolean = { | ||
| v.getReferenceAllele.length != v.getAlternateAllele.length | ||
| } | ||
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| /** | ||
| * @param rdd The RDD of variants to filter. | ||
| * @return Returns a new RDD of variants where the SNVs & MNVs have been | ||
| * removed and only INDEL variants remain. | ||
| */ | ||
| private[realigner] def filterIndels(rdd: VariantRDD): VariantRDD = { | ||
| rdd.transform(r => r.filter(discardSnvs)) | ||
| } | ||
| } |
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avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/ConsensusRealignerSuite.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.avocado.realigner | ||
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| import org.bdgenomics.adam.models.SequenceDictionary | ||
| import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD | ||
| import org.bdgenomics.adam.rdd.variant.VariantRDD | ||
| import org.bdgenomics.formats.avro.Variant | ||
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| class ConsensusRealignerSuite extends SparkRealignerSuite { | ||
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| val allowLegacyCigars = true | ||
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| def realign(rdd: AlignmentRecordRDD, | ||
| kmerLength: Int): AlignmentRecordRDD = { | ||
| ConsensusRealigner.realign(rdd, kmerLength) | ||
| } | ||
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| val snv = Variant.newBuilder | ||
| .setStart(0L) | ||
| .setReferenceAllele("A") | ||
| .setAlternateAllele("G") | ||
| .build | ||
| val mnv = Variant.newBuilder | ||
| .setStart(1L) | ||
| .setReferenceAllele("AC") | ||
| .setAlternateAllele("GT") | ||
| .build | ||
| val ins = Variant.newBuilder | ||
| .setStart(2L) | ||
| .setReferenceAllele("A") | ||
| .setAlternateAllele("ACC") | ||
| .build | ||
| val del = Variant.newBuilder | ||
| .setStart(3L) | ||
| .setReferenceAllele("GCT") | ||
| .setAlternateAllele("G") | ||
| .build | ||
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| test("filter out a snv") { | ||
| assert(!ConsensusRealigner.discardSnvs(snv)) | ||
| } | ||
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| test("filter out a mnv") { | ||
| assert(!ConsensusRealigner.discardSnvs(mnv)) | ||
| } | ||
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| test("keep an insert") { | ||
| assert(ConsensusRealigner.discardSnvs(ins)) | ||
| } | ||
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| test("keep a deletion") { | ||
| assert(ConsensusRealigner.discardSnvs(del)) | ||
| } | ||
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| sparkTest("filter snv/mnv variants out") { | ||
| val vRdd = VariantRDD(sc.parallelize(Seq(snv, mnv, ins, del)), | ||
| SequenceDictionary.empty) | ||
| val filteredVariants = ConsensusRealigner.filterIndels(vRdd) | ||
| .rdd | ||
| .collect | ||
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| val variantIds = filteredVariants.map(_.getStart) | ||
| .toSet | ||
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| assert(variantIds.size === 2) | ||
| assert(variantIds(2L)) | ||
| assert(variantIds(3L)) | ||
| } | ||
| } |
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