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/**
* The MIT License (MIT)
* Copyright (c) 2016-2017 Intel Corporation
*
* 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.
*/
#ifndef VCFDIFF_H
#define VCFDIFF_H
#include "headers.h"
#include "lut.h"
#include "vcf.h"
#include "htslib/synced_bcf_reader.h"
#include "known_field_info.h"
#include "variant_operations.h"
//Exceptions thrown
class VCFDiffException : public std::exception {
public:
VCFDiffException(const std::string m="") : msg_("VCFDiffException : "+m) { ; }
~VCFDiffException() { ; }
// ACCESSORS
/** Returns the exception message. */
const char* what() const noexcept {
return msg_.c_str();
}
private:
std::string msg_;
};
class RemapDataGoldGtIdxToTestGtIdx : public RemappedDataWrapperBase {
public:
RemapDataGoldGtIdxToTestGtIdx() {
}
void* put_address(uint64_t input_call_idx, unsigned allele_or_gt_idx) {
throw VariantOperationException("Unimplemented");
}
void build_haploid_and_diploid_gt_mappings(const unsigned num_alleles, const CombineAllelesLUT& lut) {
m_haploid_gold_genotype_idx_to_test_idx.resize(num_alleles);
auto num_diploid_gts = (num_alleles*(num_alleles+1))/2;
m_diploid_gold_genotype_idx_to_test_idx.resize(num_diploid_gts);
for (auto i=0u; i<num_alleles; ++i) {
auto lut_test_allele_idx_i = lut.get_input_idx_for_merged(0, i);
m_haploid_gold_genotype_idx_to_test_idx[i] = lut_test_allele_idx_i;
for (auto j=i; j<num_alleles; ++j) {
auto lut_test_allele_idx_j = lut.get_input_idx_for_merged(0, j);
m_diploid_gold_genotype_idx_to_test_idx[bcf_alleles2gt(i, j)] = bcf_alleles2gt(lut_test_allele_idx_i, lut_test_allele_idx_j);
}
}
}
void clear_general_mapping_vector() {
m_general_gold_genotype_idx_to_test_idx.clear();
}
void add_mapping(const uint64_t gold_gt_idx, const uint64_t input_gt_idx) {
assert(gold_gt_idx != static_cast<uint64_t>(lut_missing_value));
if (gold_gt_idx >= m_general_gold_genotype_idx_to_test_idx.size())
m_general_gold_genotype_idx_to_test_idx.resize(gold_gt_idx+1u, lut_missing_value);
m_general_gold_genotype_idx_to_test_idx[gold_gt_idx] = input_gt_idx;
}
uint64_t get_mapping(const uint64_t gold_gt_idx, const unsigned ploidy) const {
if (gold_gt_idx == static_cast<uint64_t>(lut_missing_value))
return lut_missing_value;
auto* vec_ptr = &m_haploid_gold_genotype_idx_to_test_idx;
switch (ploidy) {
case 1u:
vec_ptr = &m_haploid_gold_genotype_idx_to_test_idx;
break;
case 2u:
vec_ptr = &m_diploid_gold_genotype_idx_to_test_idx;
break;
default:
vec_ptr = &m_general_gold_genotype_idx_to_test_idx;
break;
}
auto& vec_ref = *vec_ptr;
//Might be part of padding - hence gold_gt_idx might be greater than #genotypes
return (gold_gt_idx >= vec_ref.size()) ? gold_gt_idx : vec_ref[gold_gt_idx];
}
private:
std::vector<uint64_t> m_haploid_gold_genotype_idx_to_test_idx;
std::vector<uint64_t> m_diploid_gold_genotype_idx_to_test_idx;
std::vector<uint64_t> m_general_gold_genotype_idx_to_test_idx;
};
class VCFDiffFile {
public:
VCFDiffFile(const std::string& filename, const std::string& regions="");
~VCFDiffFile();
void setup_lut(const std::set<std::string>& gold_set, const std::set<std::string>& test_set,
const int bcf_dt_type, GoldLUT& lut, const VCFDiffFile& gold);
void setup_luts(const VCFDiffFile& gold, const bool use_callsets_file_for_samples);
void set_regions_and_open_file();
void seek_and_read(const int rid, const int pos);
void read_and_advance();
void reset_field_to_line_idx_mapping() {
//-1
memset(&(m_fields_in_gold_line[0]), -1, m_fields_in_gold_line.size()*sizeof(int));
memset(&(m_fields_in_test_line[0]), -1, m_fields_in_test_line.size()*sizeof(int));
}
void print_line(std::ostream& fptr=std::cerr);
void compare_line(const bcf_hdr_t* gold_hdr, bcf1_t* gold_line);
bool compare_unequal_fields(const bcf_hdr_t* gold_hdr, const bcf1_t* gold_line, const int bcf_field_type, std::string& error_message);
template<class T1, class T2>
bool compare_unequal_vector(const bcf_hdr_t* gold_hdr, const bcf1_t* gold_line, const int bcf_field_type,
int gold_line_field_pos_idx, int test_line_field_pos_idx);
std::string create_region(const std::string& regions,
const std::unordered_map<std::string, std::pair<int64_t, int64_t>>& regions_contig_to_interval, const std::string& contig);
template<class T>
void get_ploidy(const uint64_t num_samples, const bcf_fmt_t& GT_fmt_t);
void get_ploidy_wrapper(const bcf_hdr_t* hdr, const bcf1_t* line);
public:
std::string m_filename;
std::string m_regions;
private:
bcf_srs_t* m_reader;
public:
int64_t m_num_lines_read;
bcf_hdr_t* m_hdr;
bcf1_t* m_line;
std::set<std::string> m_samples;
std::set<std::string> m_fields;
std::set<std::string> m_contigs;
GoldLUT m_samples_lut;
GoldLUT m_fields_lut;
GoldLUT m_contigs_lut;
//Fields in the line
std::vector<int> m_fields_in_gold_line;
std::vector<int> m_fields_in_test_line;
SchemaIdxToKnownVariantFieldsEnumLUT m_field_idx_to_known_field_enum;
bool m_diff_alleles_flag;
RemapDataGoldGtIdxToTestGtIdx m_gold_genotype_idx_to_test_idx;
CombineAllelesLUT m_alleles_lut;
//Temp buffer
kstring_t m_tmp_hts_string;
std::vector<unsigned> m_gold_ploidy;
bool m_contains_NON_REF_allele;
//Remapping
std::vector<int> m_gold_allele_idx_vec_for_curr_gt;
std::vector<std::pair<int, int> > m_stack;
std::vector<int> m_test_allele_idx_vec_for_curr_gt;
std::vector<uint64_t> m_remap_count_vector;
};
#endif
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