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package org.broadinstitute.hellbender.tools.funcotator;
import htsjdk.samtools.reference.ReferenceSequence;
import htsjdk.tribble.annotation.Strand;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.utils.SimpleInterval;
/**
* A simple data object to hold a comparison between a reference sequence and an alternate allele.
*
* Created by jonn on 8/30/17.
*/
public class SequenceComparison {
/**
* Bases covering the region around the variant.
* This includes bases that would overlap any of the variant or reference bases.
* (i.e. if the reference allele is 'A' and the variant is 'GCGCG', this would be
* 'ANNNNN' where 'N' is the correct base at that position in the reference sequence).
* Contains {@link SequenceComparison#referenceWindow} bases of padding before and
* after the total length.
*/
private String referenceBases = null;
/**
* The number of bases in {@link SequenceComparison#referenceBases} before the
* start of the reference Allele / variant.
*/
private Integer referenceWindow = null;
/**
* The reference coding sequence for a the transcript of this sequence comparison.
* This does NOT include introns.
* Stored in the forward reading direction. For NEGATIVE strand reads, must
* reverse complement any bases retrieved.
*/
private ReferenceSequence transcriptCodingSequence = null;
/**
* The reference coding sequence for a the transcript of this sequence comparison.
* This does NOT include introns.
* Stored in the forward reading direction. For NEGATIVE strand reads, must
* reverse complement any bases retrieved.
*/
private ReferenceSequence referenceCodingSequence = null;
/**
* The contig on which this sequence comparison occurs.
*/
private String contig = null;
/**
* The strand on which this sequence comparison occurs.
*/
private Strand strand = null;
/**
* The position (1-based, inclusive in genome coordinates relative to the start of
* {@link SequenceComparison#contig}) of the start of the reference allele / variant.
*/
private Integer alleleStart = null;
/**
* The position (1-based, inclusive) in transcript coordinates relative to the start of
* the transcript of start of the reference allele / variant.
*/
private Integer transcriptAlleleStart = null;
/**
* The position (1-based, inclusive) in coding sequence coordinates relative to the start of
* the coding region of the transcript of the start of the reference allele / variant.
* This location is obtained by concatenating the exons together and counting from the start of
* that sequence to where the reference allele / variant begins.
*/
private Integer codingSequenceAlleleStart = null;
/**
* The in-frame position (1-based, inclusive) in coding sequence coordinates relative to the start of
* the coding region of the transcript of the start of the first codon containing the reference allele / variant.
* This location is obtained by concatenating the exons together and counting from the start of
* that sequence to where the reference allele / variant begins, then moving backwards to an in-frame
* position, if necessary.
*/
private Integer alignedCodingSequenceAlleleStart = null;
/**
* The position (1-based, inclusive in genome coordinates - relative to the start of
* {@link SequenceComparison#contig}) of the start of the exon that contains the
* variant in this {@link SequenceComparison}.
*/
private Integer exonStartPosition = null;
/**
* The position (1-based, inclusive in genome coordinates - relative to the start of
* {@link SequenceComparison#contig}) of the end of the exon that contains the
* variant in this {@link SequenceComparison}.
*/
private Integer exonEndPosition = null;
/**
* The {@link String} representation of the reference allele, correctly represented for the {@link Strand} on which it appears.
*/
private String referenceAllele = null;
/**
* An in-frame sequence of bases that overlaps the given reference allele based on the raw reference genome.
* (i.e. This includes INTRONS.)
*/
private String alignedReferenceAllele = null;
/**
* An in-frame sequence of bases that overlaps the given reference allele for the coding region only.
* (i.e. This includes ONLY EXONS.)
*/
private String alignedCodingSequenceReferenceAllele = null;
/**
* The in-frame position (1-based, inclusive) of the last base of the last codon that contains the reference
* allele relative to the start of the coding sequence.
* All codons containing the reference allele can be extracted from the coding sequence using
* {@link SequenceComparison#alignedCodingSequenceAlleleStart} and {@link SequenceComparison#alignedReferenceAlleleStop}.
*/
private Integer alignedReferenceAlleleStop = null;
/**
* The {@link String} representation of the alternate allele, correctly represented for the {@link Strand} on which it appears.
*/
private String alternateAllele = null;
/**
* An in-frame sequence of bases that includes the entire alternate allele based on the reference genome.
* May span multiple codons.
* May include intron bases.
*/
private String alignedAlternateAllele = null;
/**
* An in-frame sequence of bases that includes the entire alternate allele based on the coding sequence reference.
* May span multiple codons.
*/
private String alignedCodingSequenceAlternateAllele = null;
/**
* The in-frame position (1-based, inclusive) of the last base of the last codon that contains the alternate
* allele relative to the start of the coding sequence.
* All codons containing the alternate allele can be extracted from the coding sequence using
* {@link SequenceComparison#alignedCodingSequenceAlleleStart} and {@link SequenceComparison#alignedAlternateAlleleStop}.
*/
private Integer alignedAlternateAlleleStop = null;
/**
* The fraction of Guanine and Cytosine bases in a window of a given size around a variant.
* The default windows size is {@link org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory#gcContentWindowSizeBases}.
*/
private Double gcContent = null;
/**
* Container holding information on the protein change represented by this {@link SequenceComparison} object.
*/
private ProteinChangeInfo proteinChangeInfo = null;
// =============================================================================================================
public boolean hasSequenceInfo() {
return this.transcriptCodingSequence != null;
}
public String getReferenceBases() {
return referenceBases;
}
public SequenceComparison setReferenceBases(final String referenceBases) {
this.referenceBases = referenceBases;
return this;
}
public SequenceComparison setReferenceWindow(final Integer referenceWindow) {
this.referenceWindow = referenceWindow;
return this;
}
/**
* Return the {@link ReferenceSequence} containing the coding region for the transcript of this {@link SequenceComparison}.
* This does NOT include introns.
* The reference sequence is stored in the forward reading direction.
* For NEGATIVE strand reads, must reverse complement any bases retrieved.
*/
public ReferenceSequence getTranscriptCodingSequence() {
return transcriptCodingSequence;
}
public SequenceComparison setTranscriptCodingSequence(final ReferenceSequence transcriptCodingSequence) {
this.transcriptCodingSequence = transcriptCodingSequence;
return this;
}
public String getContig() {
return contig;
}
public SequenceComparison setContig(final String contig) {
this.contig = contig;
return this;
}
public Strand getStrand() {
return strand;
}
public SequenceComparison setStrand(final Strand strand) {
if (strand == Strand.NONE) {
throw new GATKException("Cannot handle NONE strand.");
}
this.strand = strand;
return this;
}
public Integer getAlleleStart() {
return alleleStart;
}
public SequenceComparison setAlleleStart(final Integer alleleStart) {
this.alleleStart = alleleStart;
return this;
}
public Integer getTranscriptAlleleStart() {
return transcriptAlleleStart;
}
public SequenceComparison setTranscriptAlleleStart(final Integer transcriptAlleleStart) {
this.transcriptAlleleStart = transcriptAlleleStart;
return this;
}
public Integer getCodingSequenceAlleleStart() {
return codingSequenceAlleleStart;
}
public SequenceComparison setCodingSequenceAlleleStart(final Integer codingSequenceAlleleStart) {
this.codingSequenceAlleleStart = codingSequenceAlleleStart;
return this;
}
public Integer getAlignedCodingSequenceAlleleStart() {
return alignedCodingSequenceAlleleStart;
}
public SequenceComparison setAlignedCodingSequenceAlleleStart(final Integer alignedCodingSequenceAlleleStart) {
this.alignedCodingSequenceAlleleStart = alignedCodingSequenceAlleleStart;
return this;
}
public Integer getExonStartPosition() {
return exonStartPosition;
}
public Integer getExonEndPosition() {
return exonEndPosition;
}
public SequenceComparison setExonPosition( final SimpleInterval exonPosition ) {
this.exonStartPosition = exonPosition.getStart();
this.exonEndPosition = exonPosition.getEnd();
return this;
}
public String getReferenceAllele() {
return referenceAllele;
}
public SequenceComparison setReferenceAllele(final String referenceAllele) {
this.referenceAllele = referenceAllele;
return this;
}
public String getAlignedReferenceAllele() {
return alignedReferenceAllele;
}
public SequenceComparison setAlignedReferenceAllele(final String alignedReferenceAllele) {
this.alignedReferenceAllele = alignedReferenceAllele;
return this;
}
public String getAlignedCodingSequenceReferenceAllele() {
return alignedCodingSequenceReferenceAllele;
}
public SequenceComparison setAlignedCodingSequenceReferenceAllele(final String alignedCodingSequenceReferenceAllele) {
this.alignedCodingSequenceReferenceAllele = alignedCodingSequenceReferenceAllele;
return this;
}
public Integer getAlignedReferenceAlleleStop() {
return alignedReferenceAlleleStop;
}
public SequenceComparison setAlignedReferenceAlleleStop(final Integer alignedReferenceAlleleStop) {
this.alignedReferenceAlleleStop = alignedReferenceAlleleStop;
return this;
}
public String getAlternateAllele() {
return alternateAllele;
}
public SequenceComparison setAlternateAllele(final String alternateAllele) {
this.alternateAllele = alternateAllele;
return this;
}
public String getAlignedAlternateAllele() {
return alignedAlternateAllele;
}
public SequenceComparison setAlignedAlternateAllele(final String alignedAlternateAllele) {
this.alignedAlternateAllele = alignedAlternateAllele;
return this;
}
public String getAlignedCodingSequenceAlternateAllele() {
return alignedCodingSequenceAlternateAllele;
}
public SequenceComparison setAlignedCodingSequenceAlternateAllele(final String alignedCodingSequenceAlternateAllele) {
this.alignedCodingSequenceAlternateAllele = alignedCodingSequenceAlternateAllele;
return this;
}
public SequenceComparison setAlignedAlternateAlleleStop(final Integer alignedAlternateAlleleStop) {
this.alignedAlternateAlleleStop = alignedAlternateAlleleStop;
return this;
}
public Double getGcContent() {
return gcContent;
}
public SequenceComparison setGcContent(final Double gcContent) {
this.gcContent = gcContent;
return this;
}
public SequenceComparison setProteinChangeInfo(final ProteinChangeInfo p) { proteinChangeInfo = p; return this;}
public ProteinChangeInfo getProteinChangeInfo() {
return proteinChangeInfo;
}
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