htsjdk库Genotype及相关类介绍

在 HTSJDK 库中，处理基因型的主要类包括 Genotype、FastGenotype、GenotypeBuilder 以及相关的类和接口。以下是这些类和接口的详细介绍：

Genotype 类

主要功能

• 表示基因型：Genotype 类用于表示个体在特定变异位置上的基因型。基因型是对个体在变异位置上的等位基因组合的描述。
• 包含样本信息：它包括与样本相关的基因型信息，例如基因型的等位基因、深度、质量等。

源码：

/*
* Copyright (c) 2012 The Broad Institute
* 
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
* 
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* 
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/package htsjdk.variant.variantcontext;import htsjdk.tribble.util.ParsingUtils;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFUtils;import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.TreeSet;/*** This class encompasses all the basic information about a genotype.  It is immutable.** @author Mark DePristo*/
public abstract class Genotype implements Comparable<Genotype>, Serializable {public static final long serialVersionUID = 1L;/*** A list of genotype field keys corresponding to values we* manage inline in the Genotype object.  They must not appear in the* extended attributes map*/public final static Collection<String> PRIMARY_KEYS = Arrays.asList(VCFConstants.GENOTYPE_FILTER_KEY,VCFConstants.GENOTYPE_KEY,VCFConstants.GENOTYPE_QUALITY_KEY,VCFConstants.DEPTH_KEY,VCFConstants.GENOTYPE_ALLELE_DEPTHS,VCFConstants.GENOTYPE_PL_KEY);public final static String PHASED_ALLELE_SEPARATOR = "|";public final static String UNPHASED_ALLELE_SEPARATOR = "/";private final String sampleName;private GenotypeType type = null;private final String filters;protected Genotype(final String sampleName, final String filters) {this.sampleName = sampleName;this.filters = filters == null || filters.isEmpty() ? null : filters;}/*** @return the alleles for this genotype.  Cannot be null.  May be empty*/public abstract List<Allele> getAlleles();/*** @return true if any allele is REF*/public boolean hasRefAllele() {return getAlleles().stream().anyMatch(A->A.isReference());};/*** @return true if any allele is ALT, (NO_CALL are ignored)*/public boolean hasAltAllele() {return getAlleles().stream().anyMatch(A->!(A.isReference() || A.isNoCall()));};/*** Returns how many times allele appears in this genotype object?** @param allele* @return a value &gt;= 0 indicating how many times the allele occurred in this sample's genotype*/public int countAllele(final Allele allele) {int c = 0;for ( final Allele a : getAlleles() )if ( a.equals(allele) )c++;return c;}/*** Get the ith allele in this genotype** @param i the ith allele, must be &lt; the ploidy, starting with 0* @return the allele at position i, which cannot be null*/public abstract Allele getAllele(int i);/*** Are the alleles phased w.r.t. the global phasing system?** @return true if yes*/public abstract boolean isPhased();/*** What is the ploidy of this sample?** @return the ploidy of this genotype.  0 if the site is no-called.*/public int getPloidy() {return getAlleles().size();}/*** @return the sequencing depth of this sample, or -1 if this value is missing*/public abstract int getDP();/*** @return the count of reads, one for each allele in the surrounding Variant context,*      matching the corresponding allele, or null if this value is missing.  MUST*      NOT BE MODIFIED!*/public abstract int[] getAD();/*** Returns the name associated with this sample.** @return a non-null String*/public String getSampleName() {return sampleName;}/*** Returns a phred-scaled quality score, or -1 if none is available* @return*/public abstract int getGQ();/*** Does the PL field have a value?* @return true if there's a PL field value*/public boolean hasPL() {return getPL() != null;}/*** Does the AD field have a value?* @return true if there's a AD field value*/public boolean hasAD() {return getAD() != null;}/*** Does the GQ field have a value?* @return true if there's a GQ field value*/public boolean hasGQ() {return getGQ() != -1;}/*** Does the DP field have a value?* @return true if there's a DP field value*/public boolean hasDP() {return getDP() != -1;}// ---------------------------------------------------------------------------------------------------------//// The type of this genotype//// ---------------------------------------------------------------------------------------------------------/*** @return the high-level type of this sample's genotype*/public GenotypeType getType() {if ( type == null ) {type = determineType();}return type;}/*** Internal code to determine the type of the genotype from the alleles vector* @return the type*/protected GenotypeType determineType() {// TODO -- this code is slow and could be optimized for the diploid casefinal List<Allele> alleles = getAlleles();if ( alleles.isEmpty() ) {return GenotypeType.UNAVAILABLE;}boolean sawNoCall = false, sawMultipleAlleles = false;Allele firstCallAllele = null;for ( int i = 0; i < alleles.size(); i++ ) {final Allele allele = alleles.get(i);if ( allele.isNoCall() ) {sawNoCall = true;} else if ( firstCallAllele == null ) {firstCallAllele = allele;} else if ( !allele.equals(firstCallAllele) )sawMultipleAlleles = true;}if ( sawNoCall ) {if ( firstCallAllele == null )return GenotypeType.NO_CALL;return GenotypeType.MIXED;}if ( firstCallAllele == null )throw new IllegalStateException("BUG: there are no alleles present in this genotype but the alleles list is not null");return sawMultipleAlleles ? GenotypeType.HET : firstCallAllele.isReference() ? GenotypeType.HOM_REF : GenotypeType.HOM_VAR;}/*** @return true if all observed alleles are the same (regardless of whether they are ref or alt); if any alleles are no-calls, this method will return false.*/public boolean isHom()    { return isHomRef() || isHomVar(); }/*** @return true if all observed alleles are ref; if any alleles are no-calls, this method will return false.*/public boolean isHomRef() { return getType() == GenotypeType.HOM_REF; }/*** @return true if all observed alleles are alt; if any alleles are no-calls, this method will return false.*/public boolean isHomVar() { return getType() == GenotypeType.HOM_VAR; }/*** @return true if we're het (observed alleles differ); if the ploidy is less than 2 or if any alleles are no-calls, this method will return false.*/public boolean isHet() { return getType() == GenotypeType.HET; }/*** @return true if we're het (observed alleles differ) and neither allele is reference; if the ploidy is less than 2 or if any alleles are no-calls, this method will return false.*/public boolean isHetNonRef() { return (getType() == GenotypeType.HET && getAllele(0).isNonReference() && getAllele(1).isNonReference()); }/*** @return true if this genotype is not actually a genotype but a "no call" (e.g