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网站建设的商业目的,中国移动app免费下载安装,品牌网站开发背景,设计实例网站在 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…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 © 2012 The Broad Institute
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• 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
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• 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 ComparableGenotype, 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 CollectionString 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 ListAllele 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 ListAllele 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