cgatools: CnvDetailStore.hpp Source File

00001 // Copyright 2011 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_CGDATA_CNVDETAILSTORE_HPP_
00016 #define CGATOOLS_CGDATA_CNVDETAILSTORE_HPP_ 1
00017 
00019 
00020 #include "cgatools/core.hpp"
00021 #include "cgatools/reference/RangeAnnotationStore.hpp"
00022 #include "cgatools/cgdata/GenomeMetadata.hpp"
00023 
00024 namespace cgatools { namespace cgdata {
00025 
00028 struct CnvDetailData
00029 {
00030     double relativeCoverage_;
00031     std::string calledPloidy_;
00032     std::string calledLevel_;
00033     std::string bestLAF_;
00034     std::string lowLAF_;
00035     std::string highLAF_;
00036 };
00037 
00039 class CnvDetailStore :
00040     public reference::RangeAnnotationStore<CnvDetailStore, CnvDetailData>
00041 {
00042 public:
00044     CnvDetailStore(const reference::CrrFile& crr, const GenomeMetadata& exp,
00045                    bool isDiploid, bool isSomatic)
00046         : Base(crr)
00047     {
00048         if (isDiploid){
00049             if (isSomatic){
00050                 load( exp.getCnvDetailsSomaticDiploidFileName() );
00051             } else {
00052                 load( exp.getCnvDetailsDiploidFileName() );
00053             }
00054         } else {
00055             if (isSomatic){
00056                 load( exp.getCnvDetailsSomaticNondiploidFileName() );
00057             } else {
00058                 load( exp.getCnvDetailsNondiploidFileName() );
00059             }
00060         }
00061     }
00062 
00064     bool hasCalledPloidy() const { return hasCalledPloidy_; }
00065 
00067     bool hasCalledLevel() const { return hasCalledLevel_; }
00068 
00070     bool hasLAF() const { return hasLAF_; }
00071 
00075     const CnvDetailData* getBestOverlappingDetail(const reference::Range& r) const;
00076 
00077 public:
00079     void bindColumns(util::DelimitedFile& df, reference::Range& range, CnvDetailData& data);
00080 
00081 private:
00082     bool hasCalledPloidy_;
00083     bool hasCalledLevel_;
00084     bool hasLAF_;
00085 };
00086 
00087 }}
00088 
00089 #endif