Documentation cleanup and minor refactor on the consensus package. #1055
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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.adam.algorithms.consensus | ||
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| import htsjdk.samtools.{ Cigar, CigarOperator } | ||
| import org.bdgenomics.adam.models.{ ReferencePosition, ReferenceRegion } | ||
| import org.bdgenomics.adam.util.ImplicitJavaConversions._ | ||
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| /** | ||
| * Singleton object for generating consensus sequences from alignments. | ||
| * | ||
| * Provides a helper method for turning a local read alignment into a consensus. | ||
| */ | ||
| private[adam] object Consensus extends Serializable { | ||
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| /** | ||
| * Generates a consensus sequence from a local read alignment. | ||
| * | ||
| * Parses the read CIGAR and uses the read sequence to create consensuses. A | ||
| * consensus sequence is generated if an insertion or deletion is observed. | ||
| * When an insertion is observed, the insertion is cut from the read sequence | ||
| * to create the consensus. | ||
| * | ||
| * @note This method can only generate a single consensus from a read. Reads | ||
| * with more than one INDEL operator are ignored. | ||
| * | ||
| * @param sequence Read sequence. | ||
| * @param start The start position of the read alignment. | ||
|
There was a problem hiding this comment. e.g. I would prefer |
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| * @param cigar The CIGAR string for the local alignment of the read. | ||
| * @return Returns an optional consensus sequence if there is exactly one | ||
|
There was a problem hiding this comment.
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| * insertion/deletion in the read. | ||
| */ | ||
| def generateAlternateConsensus(sequence: String, | ||
| start: ReferencePosition, | ||
| cigar: Cigar): Option[Consensus] = { | ||
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| var readPos = 0 | ||
| var referencePos = start.pos | ||
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| // do we have a single indel alignment block? | ||
| if (cigar.getCigarElements.count(elem => elem.getOperator == CigarOperator.I || | ||
| elem.getOperator == CigarOperator.D) == 1) { | ||
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| // loop over elements and generate consensuses for indel blocks | ||
| cigar.getCigarElements.flatMap(cigarElement => { | ||
| cigarElement.getOperator match { | ||
| case CigarOperator.I => Some(new Consensus(sequence.substring(readPos, | ||
| readPos + cigarElement.getLength), | ||
| ReferenceRegion(start.referenceName, | ||
| referencePos, | ||
| referencePos + 1))) | ||
| case CigarOperator.D => Some(new Consensus("", | ||
| ReferenceRegion(start.referenceName, | ||
| referencePos, | ||
| referencePos + cigarElement.getLength + 1))) | ||
| case _ => { | ||
| if (cigarElement.getOperator.consumesReadBases && | ||
| cigarElement.getOperator.consumesReferenceBases) { | ||
| readPos += cigarElement.getLength | ||
| referencePos += cigarElement.getLength | ||
| } | ||
| None | ||
| } | ||
| } | ||
| }).headOption | ||
| } else { | ||
| None | ||
| } | ||
| } | ||
| } | ||
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| /** | ||
| * An INDEL alt allele to be realigned against. | ||
| * | ||
| * A consensus represents an INDEL that will be realigned against. This class | ||
| * stores the alternate allele string, and the location that this allele spans. | ||
| * | ||
| * @param consensus The alternate allele sequence. Empty if a deletion. | ||
| * @param index The reference region that this allele spans. | ||
| */ | ||
| private[adam] case class Consensus(consensus: String, index: ReferenceRegion) { | ||
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| /** | ||
| * Inserts this consensus sequence into a reference genome sequence. | ||
| * | ||
| * @throws IllegalArgumentException If the consensus doesn't overlap with the | ||
| * provided reference sequence. | ||
| * | ||
|
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| * @param reference The reference genome string of this genomic region. | ||
| * @param rr The genomic region we are splicing into. | ||
| * @return Returns the sequence corresponding to the reference with this | ||
| * allele spliced in. | ||
| */ | ||
| def insertIntoReference(reference: String, rr: ReferenceRegion): String = { | ||
| require(rr.contains(index), | ||
| "Consensus not contained in reference region: %s vs. %s.".format( | ||
| index, rr)) | ||
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| "%s%s%s".format(reference.substring(0, (index.start - rr.start).toInt), | ||
| consensus, | ||
| reference.substring((index.end - 1 - rr.start).toInt)) | ||
| } | ||
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| override def toString: String = { | ||
| if (index.start + 1 != index.end) { | ||
| "Deletion over " + index.toString | ||
| } else { | ||
| "Inserted " + consensus + " at " + index.toString | ||
| } | ||
| } | ||
| } | ||
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@paramcomments don't need to be full sentences