cgatools: Locus.hpp Source File

00001 // Copyright 2010 Complete Genomics, Inc.
00002 //
00003 // Licensed under the Apache License, Version 2.0 (the "License"); you
00004 // may not use this file except in compliance with the License. You
00005 // may obtain a copy of the License at
00006 //
00007 // http://www.apache.org/licenses/LICENSE-2.0
00008 //
00009 // Unless required by applicable law or agreed to in writing, software
00010 // distributed under the License is distributed on an "AS IS" BASIS,
00011 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
00012 // implied. See the License for the specific language governing
00013 // permissions and limitations under the License.
00014 
00015 #ifndef CGATOOLS_VARIANTS_LOCUS_HPP_
00016 #define CGATOOLS_VARIANTS_LOCUS_HPP_ 1
00017 
00019 
00020 #include "cgatools/core.hpp"
00021 #include "cgatools/variants/Call.hpp"
00022 #include "cgatools/variants/Allele.hpp"
00023 #include "cgatools/reference/CrrFile.hpp"
00024 
00025 #include <map>
00026 
00027 namespace cgatools { namespace variants {
00028 
00031     class Locus
00032     {
00033         typedef reference::CrrFile CrrFile;
00034         typedef reference::Location Location;
00035         typedef reference::Range Range;
00036     public:
00038         Locus()
00039             : crr_(0)
00040         {
00041         }
00042 
00046         Locus(const CrrFile& crr)
00047             : crr_(&crr)
00048         {
00049         }
00050 
00053         Locus(const Locus& other);
00054 
00057         Locus& operator=(const Locus& other);
00058 
00061         const std::vector<Call>& getCalls() const
00062         {
00063             return calls_;
00064         }
00065 
00068         std::vector<Call>& getCalls()
00069         {
00070             return calls_;
00071         }
00072 
00074         const std::vector<Allele>& getAlleles() const
00075         {
00076             return alleles_;
00077         }
00078 
00080         const Range& getRange() const
00081         {
00082             return range_;
00083         }
00084 
00086         void setRange(const Range& range);
00087 
00089         const CrrFile& getReference() const
00090         {
00091             return *crr_;
00092         }
00093 
00095         boost::uint32_t getId() const;
00096 
00099         void setId(boost::uint32_t locusId);
00100 
00102         boost::uint16_t getPloidy() const;
00103 
00105         void setHapLink(size_t alleleOffset, const std::string& hapLink);
00106 
00109         bool isRefCallLocus() const;
00110 
00112         bool isNoCallLocus() const;
00113 
00116         bool isRefConsistent() const;
00117 
00120         bool hasNoCalls() const;
00121 
00123         void clearCalls();
00124 
00126         void addCall(const Call& call);
00127 
00130         void initFromCalls(bool relaxedReferenceValidation = true);
00131 
00136         void locationCalls(const Location& loc, std::vector< std::pair<char, const Call*> >& calls) const;
00137 
00139         std::string getType() const;
00140 
00142         std::string getZygosity() const;
00143 
00146         void reorderAlleles();
00147 
00150         void writeAsOneLine(std::ostream& out, bool writeExtras = true, char sep = '\t') const;
00151 
00152         static void writeOneLineFileHeader(std::ostream& out, char sep = '\t');
00153     private:
00154         void validateCalls(bool relaxedReferenceValidation) const;
00155         void validateAllelesAndInitRange();
00156         void callError (const std::string&, const Call&) const;
00157         void locusError(const std::string&) const;
00158 
00159         Range range_;
00160         const CrrFile* crr_;
00161         std::vector<Call> calls_;
00162         std::vector<Allele> alleles_;
00163 
00164     public:
00166         std::vector<std::string> extras_;
00167     };
00168 
00169     std::ostream& operator<<(std::ostream& out, const Locus& locus);
00170 
00171 } } // cgatools::variants
00172 
00173 #endif // CGATOOLS_VARIANTS_LOCUS_HPP_