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Factoring out Spark realigner tests.
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avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/SparkRealignerSuite.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, | ||
| SequenceRecord, | ||
| RecordGroup, | ||
| RecordGroupDictionary | ||
| } | ||
| import org.bdgenomics.adam.rdd.ADAMContext._ | ||
| import org.bdgenomics.adam.rdd.read.{ AlignedReadRDD, AlignmentRecordRDD } | ||
| import org.bdgenomics.avocado.AvocadoFunSuite | ||
| import org.bdgenomics.formats.avro.AlignmentRecord | ||
|
|
||
| trait SparkRealignerSuite extends AvocadoFunSuite { | ||
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| def realign(rdd: AlignmentRecordRDD, | ||
| kmerLength: Int): AlignmentRecordRDD | ||
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| def makeAndRealignRdd(reads: Seq[AlignmentRecord], | ||
| kmerLength: Int): Array[AlignmentRecord] = { | ||
| val gRdd = AlignedReadRDD(sc.parallelize(reads), | ||
| SequenceDictionary(SequenceRecord("ctg", 50L)), | ||
| RecordGroupDictionary(Seq(RecordGroup("rg", "rg")))) | ||
|
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| // realign the genomic rdd | ||
| val realignedRdd = realign(gRdd, kmerLength) | ||
|
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| // collect the reads | ||
| realignedRdd.rdd.collect() | ||
| } | ||
|
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| sparkTest("realign a set of reads around an insert") { | ||
| // insertion sequence: | ||
| // ins: AATGAGACTTACATCATTAAAACCGTGTGGACACA | ||
| // ref: AATGAGACTTACATCATTAA__CCGTGTGGACACA | ||
| val sequence = "AATGAGACTTACATCATTAAAACCGTGTGGACACA" | ||
| val insertStart = 20 | ||
| val readLength = insertStart + 6 + 2 | ||
|
|
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| // generate 7 reads with a 6bp flank | ||
| val reads = (0 until 7).map(rId => { | ||
| val basesBeforeInsert = insertStart - rId | ||
| val basesAfterInsert = 6 + rId | ||
|
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| AlignmentRecord.newBuilder() | ||
| .setReadName(rId.toString) | ||
| .setContigName("ctg") | ||
| .setRecordGroupName("rg") | ||
| .setReadMapped(true) | ||
| .setSequence(sequence.drop(rId).take(readLength)) | ||
| .setStart(rId.toLong) | ||
| .setEnd((rId + readLength - 2 + 1).toLong) | ||
| .setCigar("%dM2I%dM".format(basesBeforeInsert, basesAfterInsert)) | ||
| .setMismatchingPositions((readLength - 2).toString) | ||
| .build() | ||
| }) | ||
|
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| // make into a genomic rdd | ||
| val newReads = makeAndRealignRdd(reads, 6) | ||
|
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| assert(newReads.size === 7) | ||
| newReads.foreach(r => { | ||
| val rId = r.getReadName.toInt | ||
|
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| // these values are different from above because original alignments were | ||
| // not left justified | ||
| val basesBeforeInsert = insertStart - rId - 2 | ||
| val basesAfterInsert = 8 + rId | ||
|
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| assert(r.getCigar === "%d=2I%d=".format(basesBeforeInsert, basesAfterInsert)) | ||
| assert(r.getMismatchingPositions === (readLength - 2).toString) | ||
| }) | ||
| } | ||
|
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| sparkTest("realign a set of reads around a deletion") { | ||
| // deletion sequence: | ||
| // del: AGGTCTGAATGAGACTTA__TCATTAACCGTGTGGACACA | ||
| // ref: AGGTCTGAATGAGACTTACATCATTAACCGTGTGGACACA | ||
| val sequence = "AGGTCTGAATGAGACTTATCATTAACCGTGTGGACACA" | ||
| val deleteStart = 18 | ||
| val readLength = deleteStart + 8 | ||
|
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| // generate 10 reads with a 8bp flank | ||
| val reads = (0 until 10).map(rId => { | ||
| val basesBeforeDelete = deleteStart - rId | ||
| val basesAfterDelete = 8 + rId | ||
|
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| AlignmentRecord.newBuilder() | ||
| .setReadName(rId.toString) | ||
| .setContigName("ctg") | ||
| .setRecordGroupName("rg") | ||
| .setReadMapped(true) | ||
| .setSequence(sequence.drop(rId).take(readLength)) | ||
| .setStart(rId.toLong) | ||
| .setEnd((rId + readLength + 2 + 1).toLong) | ||
| .setCigar("%dM2D%dM".format(basesBeforeDelete, basesAfterDelete)) | ||
| .setMismatchingPositions("%d^CA%d".format(basesBeforeDelete, basesAfterDelete)) | ||
| .build() | ||
| }) | ||
|
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| // make into a genomic rdd | ||
| val newReads = makeAndRealignRdd(reads, 8) | ||
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| assert(newReads.size === 10) | ||
| newReads.foreach(r => { | ||
| val rId = r.getReadName.toInt | ||
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| // these values are different from above because original alignments were | ||
| // not left justified | ||
| val basesBeforeDelete = deleteStart - rId - 1 | ||
| val basesAfterDelete = 9 + rId | ||
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| assert(r.getCigar === "%d=2D%d=".format(basesBeforeDelete, basesAfterDelete)) | ||
| assert(r.getMismatchingPositions === "%d^AC%d".format(basesBeforeDelete, basesAfterDelete)) | ||
| }) | ||
| } | ||
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| sparkTest("realigning a read with a repeat will return the original read") { | ||
| val read = AlignmentRecord.newBuilder() | ||
| .setReadName("A_READ") | ||
| .setReadMapped(true) | ||
| .setStart(10L) | ||
| .setEnd(17L) | ||
| .setSequence("TCAAAAAAGG") | ||
| .setCigar("3M4I3M") | ||
| .setMismatchingPositions("6") | ||
| .build() | ||
|
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| // make into a genomic rdd | ||
| val newReads = makeAndRealignRdd(Seq(read), 3) | ||
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| // should have one read | ||
| assert(newReads.size === 1) | ||
| assert(newReads.head === read) | ||
| } | ||
| } |