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main.hpp
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#ifndef main_hpp_INCLUDED
#define main_hpp_INCLUDED
#include "bcf_formats.step1.hpp" // auto-generated
#include "CmdLineArgs.hpp"
#include "common.hpp"
#include "iohts.hpp"
#include "logging.hpp"
#include "main_consensus.hpp"
#include "main_conversion.hpp"
#include "MolecularID.hpp"
#include "htslib/faidx.h"
#include "htslib/hts.h"
#include "htslib/sam.h"
#include "htslib/synced_bcf_reader.h"
#include <algorithm>
#include <array>
#include <iostream>
#include <map>
#include <set>
#include <tuple>
#include <vector>
#include <assert.h>
#include <limits.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
class HapLink {
public:
std::basic_string<std::pair<uvc1_refgpos_t, AlignmentSymbol>> pos_symb_string;
std::array<uvc1_readnum_t, 2> fr_cnts;
std::array<uvc1_readnum_t, 2> other_hap_cnts;
HapLink(
std::basic_string<std::pair<uvc1_refgpos_t, AlignmentSymbol>> pos_symb_string_1,
std::array<uvc1_readnum_t, 2> fr_cnts_1,
std::array<uvc1_readnum_t, 2> other_hap_cnt_1) {
pos_symb_string = pos_symb_string_1;
fr_cnts = fr_cnts_1;
other_hap_cnts = other_hap_cnt_1;
};
};
// T=uvc1_readnum_t for deletion and T=string for insertion
template <class T>
std::pair<uvc1_readnum_t, T>
indelToData_getMajority(const std::map<T, uvc1_readnum_t> & indel2cnt) {
uvc1_readnum_t maxcnt = 0;
T argmaxcnt = T();
for (const auto ic : indel2cnt) {
if (ic.second > maxcnt ||
((ic.second == maxcnt) && (ic.first > argmaxcnt))) {
maxcnt = ic.second;
argmaxcnt = ic.first;
}
}
return std::make_pair(maxcnt, argmaxcnt);
}
template <class T>
uvc1_readnum_t
posToIndelToData_get(const std::map<uvc1_readnum_t, std::map<T, uvc1_readnum_t>> & pos2indel2data, const uvc1_readnum_t refpos, const T & indel, uvc1_readnum_t default1 = 0, uvc1_readnum_t default2 = 0) {
if (pos2indel2data.find(refpos) == pos2indel2data.end()) { return default1; }
if (pos2indel2data.at(refpos).find(indel) == pos2indel2data.at(refpos).end()) { return default2; }
return pos2indel2data.at(refpos).at(indel);
}
template <class T>
void
posToIndelToCount_inc(std::map<uvc1_refgpos_t, std::map<T, uvc1_readnum_t>> & pos2indel2count, uvc1_readpos_t pos, const T indel, uvc1_readnum_t incvalue = 1) {
assertUVC(incvalue > 0);
auto pos2indel2count4it = pos2indel2count.insert(std::make_pair(pos, std::map<T, uvc1_readnum_t>()));
auto indel2count4it = pos2indel2count4it.first->second.insert(std::make_pair(indel, 0));
indel2count4it.first->second += incvalue;
assertUVC (posToIndelToData_get(pos2indel2count, pos, indel) > 0);
}
template <class T>
T
posToIndelToCount_updateByConsensus(std::map<uvc1_refgpos_t, std::map<T, uvc1_readnum_t>> & dst, const std::map<uvc1_refgpos_t, std::map<T, uvc1_readnum_t>> & src, uvc1_readnum_t epos, uvc1_readnum_t incvalue = 1) {
const auto pos2indel2count4it = src.find(epos);
assertUVC(pos2indel2count4it != src.end());
auto indel2count = pos2indel2count4it->second;
const T & src_indel = (indel2count.size() > 1 ? (indelToData_getMajority(indel2count).second) : indel2count.begin()->first);
// The following code generates null-valued InDels if more than one InDel is found, which is not intended.
// const T & src_indel = (indel2count.size() > 1 ? T() : indel2count.begin()->first);
assertUVC (indel2count.begin()->second > 0);
posToIndelToCount_inc<T>(dst, epos, src_indel, incvalue);
return src_indel;
}
// For reason of commenting-out this method, please check the method updateByRepresentative that calls this method
/*
template <bool TIsIncVariable, class T>
uvc1_readnum_t
posToIndelToCount_updateByRepresentative(std::map<uvc1_readnum_t, std::map<T, uvc1_readnum_t>> & dst, const std::map<uvc1_readnum_t, std::map<T, uvc1_readnum_t>> & src, uvc1_readnum_t epos, uvc1_readnum_t incvalue = 1) {
const auto pos2indel2count4it = src.find(epos);
assertUVC(pos2indel2count4it != src.end());
T max_indel;
uvc1_readnum_t max_count = 0;
uvc1_readnum_t sum_count = 0;
for (auto indel2count : pos2indel2count4it->second) {
auto indel = indel2count.first;
auto count = indel2count.second;
if (count > max_count) {
max_indel = indel;
max_count = count;
}
if (TIsIncVariable) {sum_count += count; }
}
assertUVC(0 < max_count);
if (TIsIncVariable) {
posToIndelToCount_inc<T>(dst, epos, max_indel, sum_count);
} else {
posToIndelToCount_inc<T>(dst, epos, max_indel, incvalue);
}
return max_count;
}
*/
template <class T>
void
posToIndelToCount_updateBySummation(std::map<uvc1_readnum_t, std::map<T, uvc1_readnum_t>> & dst, const std::map<uvc1_readnum_t, std::map<T, uvc1_readnum_t>> & src) {
for (auto src_pos2indel2count4it : src) {
auto src_pos = src_pos2indel2count4it.first;
auto src_indel2count = src_pos2indel2count4it.second;
for (auto src_indel2count4it : src_indel2count) {
assertUVC(src_indel2count4it.second > 0 || !(
std::cerr << src_indel2count4it.second << " > 0 failed for the key " << src_indel2count4it.first << " at position " << src_pos << std::endl
));
posToIndelToCount_inc<T>(dst, src_pos, src_indel2count4it.first, src_indel2count4it.second);
}
}
}
void
posToIndelToCount_DlenToDseq(std::map<uvc1_readnum_t, std::map<std::string, uvc1_readnum_t>> & dst, const std::map<uvc1_readnum_t, std::map<uvc1_readnum_t, uvc1_readnum_t>> & src,
const std::string & refchars, uvc1_readnum_t incluBegPos) {
for (auto src_pos2indel2count4it : src) {
uvc1_readnum_t src_pos = src_pos2indel2count4it.first;
auto src_del2count = src_pos2indel2count4it.second;
for (auto src_del2count4it : src_del2count) {
std::string dseq = refchars.substr(src_pos - incluBegPos, src_del2count4it.first);
posToIndelToCount_inc(dst, src_pos, dseq, src_del2count4it.second);
}
}
}
#define INS_N_ANCHOR_BASES 1 // https://www.ncbi.nlm.nih.gov/pmc/articles/PMC149199/
#define TVN_MICRO_VQ_DELTA 3
#define TIN_CONTAM_MICRO_VQ_DELTA 0
#define BAM_PHREDI(b, i) (bam_get_qual((b))[(i)])
const bcfrec::BcfFormat FORMAT_UNCOV = bcfrec::BcfFormat();
const RevComplement THE_REV_COMPLEMENT;
enum ValueType {
SYMBOL_COUNT_SUM,
BASE_QUALITY_MAX, // https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302405/
VALUE_TYPE_END,
};
// is not WGS (i.e., is hybrid-capture-WES or amplicon-PCR)
template <class T1, class T2>
inline bool
does_fmt_imply_short_frag(const T1 & fmt, const T2 wgs_min_avg_fragsize) {
return (fmt.APLRI[0] + fmt.APLRI[2]) < int64mul(fmt.APLRI[1] + fmt.APLRI[3], wgs_min_avg_fragsize);
}
std::pair<uvc1_readnum_t, std::string>
read_family_con_ampl_getMajority_clip(const auto &read_family_con_ampl, const uvc1_refgpos_t epos) {
std::map<std::string, uvc1_readnum_t> indel2readnum = { {"", 0} };
auto p2e2d = read_family_con_ampl.getPosToCseqToData();
if (p2e2d.find(epos) != p2e2d.end()) {
std::map<std::string, uvc1_readnum_t> indel2data = p2e2d.find(epos)->second;
indel2readnum.insert(indel2data.begin(), indel2data.end());
}
return indelToData_getMajority(indel2readnum);
}
std::pair<uvc1_readnum_t, std::string>
read_family_con_ampl_getMajority_ins(const auto &read_family_con_ampl, const uvc1_refgpos_t epos) {
std::map<std::string, uvc1_readnum_t> indel2readnum = { {"", 0} };
for (const AlignmentSymbol s : INS_SYMBOLS) {
auto p2e2d = read_family_con_ampl.getPosToIseqToData(s);
if (p2e2d.find(epos) != p2e2d.end()) {
std::map<std::string, uvc1_readnum_t> indel2data = p2e2d.find(epos)->second;
indel2readnum.insert(indel2data.begin(), indel2data.end());
}
}
return indelToData_getMajority(indel2readnum);
}
std::pair<uvc1_readnum_t, uvc1_refgpos_t>
read_family_con_ampl_getMajority_del(const auto &read_family_con_ampl, const uvc1_refgpos_t epos) {
std::map<uvc1_refgpos_t, uvc1_readnum_t> indel2readnum = { {0, 0} };
for (const AlignmentSymbol s : DEL_SYMBOLS) {
auto p2e2d = read_family_con_ampl.getPosToDlenToData(s);
if (p2e2d.find(epos) != p2e2d.end()) {
std::map<uvc1_refgpos_t, uvc1_readnum_t> indel2data = p2e2d.find(epos)->second;
indel2readnum.insert(indel2data.begin(), indel2data.end());
}
}
return indelToData_getMajority(indel2readnum);
}
struct PhredMutationTable {
const uvc1_qual_t transition_CG_TA;
const uvc1_qual_t transition_AT_CG;
const uvc1_qual_t transversion_CG_AT;
const uvc1_qual_t transversion_other;
const uvc1_qual_t indel_open;
const uvc1_qual_t indel_ext;
uvc1_qual_t all_mutation_inc;
PhredMutationTable(
const uvc1_qual_t transition_CG_TA,
const uvc1_qual_t transition_AT_CG,
const uvc1_qual_t transversion_CG_AT,
const uvc1_qual_t transversion_other,
const uvc1_qual_t indel_open,
const uvc1_qual_t indel_ext,
const bool is_rescued)
:
transition_CG_TA(transition_CG_TA),
transition_AT_CG(transition_AT_CG),
transversion_CG_AT(transversion_CG_AT),
transversion_other(transversion_other),
indel_open(indel_open),
indel_ext(indel_ext),
all_mutation_inc(is_rescued ? 3 : 0)
{ }
uvc1_qual_t toPhredErrRateRaw(const AlignmentSymbol con_symbol, const AlignmentSymbol alt_symbol) const {
if (isSymbolIns(con_symbol) || isSymbolDel(con_symbol)) {
return indel_open;
} else if (con_symbol == LINK_M) {
if (LINK_D1 == alt_symbol || LINK_I1 == alt_symbol) {
return indel_open;
} else if (LINK_D2== alt_symbol || LINK_I2 == alt_symbol) {
return indel_open + indel_ext * 1;
} else {
return indel_open + indel_ext * 2;
}
} else if ((con_symbol == BASE_C && alt_symbol == BASE_T) || (con_symbol == BASE_G && alt_symbol == BASE_A)) {
return transition_CG_TA;
} else if ((con_symbol == BASE_A && alt_symbol == BASE_G) || (con_symbol == BASE_T && alt_symbol == BASE_C)) {
return transition_AT_CG;
} else if ((con_symbol == BASE_C && alt_symbol == BASE_A) || (con_symbol == BASE_G && alt_symbol == BASE_T)) {
return transversion_CG_AT;
} else {
return transversion_other;
}
}
uvc1_qual_t toPhredErrRate(const AlignmentSymbol con_symbol, const AlignmentSymbol alt_symbol) const {
return toPhredErrRateRaw(con_symbol, alt_symbol) + all_mutation_inc;
}
};
constexpr bool
is_mut_transition(const AlignmentSymbol con_symbol, const AlignmentSymbol alt_symbol) {
return ((con_symbol == BASE_C && alt_symbol == BASE_T) || (con_symbol == BASE_G && alt_symbol == BASE_A)
|| (con_symbol == BASE_T && alt_symbol == BASE_C) || (con_symbol == BASE_A && alt_symbol == BASE_G)
);
}
const uvc1_refgpos_t SYMBOL_TO_INDEL_N_UNITS[] = {
[BASE_A] = 0, [BASE_C] = 0, [BASE_G] = 0, [BASE_T] = 0, [BASE_N] = 0,
[BASE_NN] = 0,
[LINK_M] = 0,
[LINK_D3P] = -3, [LINK_D2] = -2, [LINK_D1] = -1,
[LINK_I3P] = 3, [LINK_I2] = 2, [LINK_I1] = 1,
[LINK_NN] = 0,
[END_ALIGNMENT_SYMBOLS] = 0,
};
template <class T>
class TDistribution {
protected:
std::array<T, NUM_ALIGNMENT_SYMBOLS> symbol2data;
};
typedef uvc1_readnum_t molcount_t;
template <class TB2C>
class GenericSymbol2Bucket2Count : TDistribution<TB2C> {
public:
molcount_t
getSymbolBucketCount(AlignmentSymbol symbol, size_t bucket) const {
assertUVC(bucket < NUM_BUCKETS);
return this->symbol2data[symbol][bucket];
};
const TB2C &
getSymbolCounts(AlignmentSymbol symbol) const {
return this->symbol2data[symbol];
};
void
incSymbolBucketCount(AlignmentSymbol symbol, size_t bucket, uvc1_qual_t increment) {
assertUVC(bucket < NUM_BUCKETS || !fprintf(stderr, "%lu < %d failed!", bucket, NUM_BUCKETS));
this->symbol2data[symbol].at(bucket) += increment;
};
const TB2C
vectorsumBySymbolType(const SymbolType symboltype) const {
TB2C ret = {0};
for (AlignmentSymbol symbol : SYMBOL_TYPE_TO_SYMBOLS[symboltype]) {
for (size_t i = 0; i < this->symbol2data[symbol].size(); i++) {
ret[i] += this->getSymbolBucketCount(symbol, i);
}
}
return ret;
};
void
clearSymbolBucketCount() {
assertUVC(sizeof(TB2C) * NUM_ALIGNMENT_SYMBOLS == sizeof(this->symbol2data) || !fprintf(stderr, "%lu * %u != %lu\n", sizeof(TB2C), NUM_ALIGNMENT_SYMBOLS, sizeof(this->symbol2data)));
for (size_t i = 0; i < NUM_ALIGNMENT_SYMBOLS; i++) {
for (size_t j = 0; j < this->symbol2data[0].size(); j++) {
this->symbol2data[i][j] = 0;
}
}
};
};
template <class TInteger>
class GenericSymbol2Count : TDistribution<TInteger> {
public:
TInteger
getSymbolCount(AlignmentSymbol symbol) const {
return this->symbol2data[symbol];
};
template <ValueType TUpdateType = SYMBOL_COUNT_SUM>
int // update_max_inc : high GC : 3, even distribution of nucleotides : 6, conservative : 0
incSymbolCount(const AlignmentSymbol symbol, const TInteger increment, const TInteger update_max_inc = 0) {
STATIC_ASSERT_WITH_DEFAULT_MSG(BASE_QUALITY_MAX == TUpdateType || SYMBOL_COUNT_SUM == TUpdateType);
if (SYMBOL_COUNT_SUM == TUpdateType) {
this->symbol2data[symbol] += increment;
} else {
this->symbol2data[symbol] = MAX(this->symbol2data[symbol], increment) + (this->symbol2data[symbol] ? update_max_inc : 0);
}
return 0;
};
const TInteger
_sumBySymbolType(AlignmentSymbol beg, AlignmentSymbol end) const {
assertUVC (beg <= end);
TInteger alpha_sum = 0;
for (AlignmentSymbol symb = beg; symb <= end; symb = AlignmentSymbol(((uvc1_unsigned_int_t)symb) + 1)) {
alpha_sum += this->symbol2data[symb];
}
return alpha_sum;
};
const TInteger
sumBySymbolType(const SymbolType symboltype) const {
if (symboltype == BASE_SYMBOL) {
return this->_sumBySymbolType(BASE_A, BASE_NN);
} else if (symboltype == LINK_SYMBOL) {
return this->_sumBySymbolType(LINK_M, LINK_NN);
} else {
abort();
return -1;
}
};
template <bool TIsBestKeptAsCons>
int
_fillConsensusCounts(
AlignmentSymbol & count_argmax, uvc1_qual_t & count_max, uvc1_qual_t & count_sum,
AlignmentSymbol incluBeg, AlignmentSymbol incluEnd) const {
assertUVC (incluBeg <= incluEnd);
count_argmax = incluEnd; // assign with the value AlignmentSymbol(NUM_ALIGNMENT_SYMBOLS) to flag for error
count_max = 0;
count_sum = 0;
for (AlignmentSymbol symb = incluBeg; symb <= incluEnd; symb = AlignmentSymbol(((uvc1_unsigned_int_t)symb) + 1)) {
if (TIsBestKeptAsCons) {
if (count_max < this->symbol2data[symb] || (LINK_M == count_argmax && (0 < this->symbol2data[symb]))) {
count_argmax = symb;
count_max = this->symbol2data[symb];
count_sum = count_max;
}
} else {
if (count_max < this->symbol2data[symb]) {
count_argmax = symb;
count_max = this->symbol2data[symb];
}
count_sum += this->symbol2data[symb];
}
}
assertUVC((incluBeg <= count_argmax && count_argmax <= incluEnd) || !fprintf(stderr, "The value %u is not between %u and %u", count_argmax, incluBeg, incluEnd));
return 0;
};
template <bool TIsBestKeptAsCons = true, bool TIgnorePaddedDel = false>
int
fillConsensusCounts(
AlignmentSymbol & count_argmax, uvc1_qual_t & count_max, uvc1_qual_t & count_sum,
const SymbolType symboltype) const {
if (symboltype == BASE_SYMBOL) {
return this->template _fillConsensusCounts<false >(count_argmax, count_max, count_sum, BASE_A, (TIgnorePaddedDel ? BASE_T : BASE_NN));
} else if (symboltype == LINK_SYMBOL) {
return this->template _fillConsensusCounts<TIsBestKeptAsCons>(count_argmax, count_max, count_sum, LINK_M, LINK_NN);
} else {
abort();
return -1;
}
};
template<bool TIsBestKeptAsCons>
AlignmentSymbol
_updateByConsensus(const GenericSymbol2Count<TInteger> & thatSymbol2Count,
const SymbolType symboltype, const AlignmentSymbol ambig_pos, const uvc1_qual_t incvalue) {
AlignmentSymbol argmax_count = END_ALIGNMENT_SYMBOLS; // AlignmentSymbol(0) is not fully correct
uvc1_qual_t max_count = 0;
uvc1_qual_t sum_count = 0;
thatSymbol2Count.template fillConsensusCounts<TIsBestKeptAsCons>(argmax_count, max_count, sum_count, symboltype);
if (max_count > 0) {
if ((sum_count - max_count) == 0) {
this->symbol2data[argmax_count] += incvalue;
return argmax_count;
} else {
this->symbol2data[ambig_pos] += incvalue;
return ambig_pos;
}
} else {
return END_ALIGNMENT_SYMBOLS;
}
};
template<bool TIsBestKeptAsCons = true>
std::array<AlignmentSymbol, 2>
updateByConsensus(const GenericSymbol2Count<TInteger> & thatSymbol2Count, uvc1_qual_t incvalue = 1) {
AlignmentSymbol baseSymb = this->template _updateByConsensus<false >(thatSymbol2Count, BASE_SYMBOL, BASE_NN, incvalue);
AlignmentSymbol linkSymb = this->template _updateByConsensus<TIsBestKeptAsCons>(thatSymbol2Count, LINK_SYMBOL, LINK_NN, incvalue);
return {baseSymb, linkSymb};
};
// For reason of commenting-out this method, please check the identically named method that calls it
/*
template <bool TIsIncVariable = true>
AlignmentSymbol
updateByRepresentative(const GenericSymbol2Count<TInteger> & other, uvc1_qual_t incvalue = 1) {
AlignmentSymbol consalpha;
uvc1_qual_t countalpha, totalalpha;
for (SymbolType symboltype : SYMBOL_TYPE_ARR) {
other.fillConsensusCounts(consalpha, countalpha, totalalpha, symboltype);
if (countalpha > 0) {
this->symbol2data[consalpha] += (TIsIncVariable ? totalalpha : incvalue);
}
}
return consalpha;
};
*/
template <bool TIsBestKeptAsCons = true>
int
updateByFiltering(
std::array<AlignmentSymbol, NUM_SYMBOL_TYPES> & con_symbols,
const GenericSymbol2Count<TInteger> & other,
const bool is_padded_del_ignored,
const std::array<uvc1_qual_t, NUM_SYMBOL_TYPES> thres = {{0}},
const uvc1_qual_t incvalue = 1) {
int ret = 0;
AlignmentSymbol consalpha;
uvc1_qual_t countalpha, totalalpha;
for (SymbolType symboltype : SYMBOL_TYPE_ARR) {
if (LINK_SYMBOL == symboltype) {
other.template fillConsensusCounts<TIsBestKeptAsCons>(consalpha, countalpha, totalalpha, symboltype);
} else {
if (is_padded_del_ignored) {
other.template fillConsensusCounts<false, true>(consalpha, countalpha, totalalpha, symboltype);
} else {
other.template fillConsensusCounts<false, false>(consalpha, countalpha, totalalpha, symboltype);
}
}
auto adjcount = MAX(countalpha * 2, totalalpha) - totalalpha;
if (adjcount >= thres[symboltype] && adjcount > 0) {
this->symbol2data[consalpha] += incvalue;
ret++;
}
con_symbols[symboltype] = consalpha;
}
return ret;
};
int
updateByMajorMinusMinor(
std::array<AlignmentSymbol, NUM_SYMBOL_TYPES> & con_symbols,
std::array<uvc1_qual_t, NUM_SYMBOL_TYPES> & con_counts,
const GenericSymbol2Count<TInteger> & other) {
int ret = 0;
AlignmentSymbol consalpha;
uvc1_qual_t countalpha, totalalpha;
for (SymbolType symboltype : SYMBOL_TYPE_ARR) {
if (LINK_SYMBOL == symboltype) {
other.template fillConsensusCounts<true >(consalpha, countalpha, totalalpha, symboltype);
} else {
other.template fillConsensusCounts<false>(consalpha, countalpha, totalalpha, symboltype);
}
auto adjcount = MAX(countalpha * 2, totalalpha) - totalalpha;
if (adjcount > 0) {
this->symbol2data[consalpha] += adjcount;
ret++;
}
con_symbols[symboltype] = consalpha;
con_counts[symboltype] = adjcount;
}
return ret;
};
};
template<class T>
class CoveredRegion {
protected:
std::vector<T> idx2symbol2data;
std::array<std::map<uvc1_refgpos_t, std::map<uvc1_readpos_t , uvc1_readnum_t>>, NUM_INS_SYMBOLS> pos2dlen2data;
std::array<std::map<uvc1_refgpos_t, std::map<std::string, uvc1_readnum_t>>, NUM_DEL_SYMBOLS> pos2iseq2data;
std::array<ConsensusBlockSet, NUM_CONSENSUS_BLOCK_CIGAR_TYPES> conblocksets;
public:
const uvc1_refgpos_t tid;
const uvc1_refgpos_t incluBegPosition; // where end_pos = incluBegPosition + idx2symbol2data.size()
CoveredRegion() {};
CoveredRegion(uvc1_refgpos_t tid, uvc1_refgpos_t beg, uvc1_refgpos_t end): tid(tid), incluBegPosition(beg) {
assertUVC (beg < end || !fprintf(stderr, "assertion %d < %d failed!\n", beg, end));
this->idx2symbol2data = std::vector<T>(end-beg); // end should be real end position plus one
for (const auto conblock_cigartype : ALL_CONSENSUS_BLOCK_CIGAR_TYPES) {
if (is_ConsensusBlockCigarType_right2left(conblock_cigartype)) {
conblocksets[conblock_cigartype].setIsRightToLeft(true);
}
}
};
T &
getRefByPos(const uvc1_refgpos_t pos, const bam1_t *bam = NULL) {
assertUVC(pos >= this->incluBegPosition || !fprintf(stderr, "%d >= %d failed for qname %s !\n", pos, this->incluBegPosition, (NULL != bam ? bam_get_qname(bam) : "?")));
uvc1_refgpos_t pos2 = pos - this->incluBegPosition;
assertUVC(pos2 < UNSIGN2SIGN(idx2symbol2data.size()) || !fprintf(stderr, "%d < %d failed for qname %s !\n", pos, this->incluBegPosition + (uvc1_refgpos_t)(idx2symbol2data.size()), (NULL != bam ? bam_get_qname(bam) : "?")));
return this->idx2symbol2data[pos2];
};
const T &
getByPos(const uvc1_refgpos_t pos, const bam1_t *bam = NULL) const {
assertUVC(pos >= this->incluBegPosition || !fprintf(stderr, "%d >= %d failed for qname %s !\n", pos, this->incluBegPosition, (NULL != bam ? bam_get_qname(bam) : "?")));
uvc1_refgpos_t pos2 = pos - this->incluBegPosition;
assertUVC((pos2 < UNSIGN2SIGN(idx2symbol2data.size())) || !fprintf(stderr, "%d < %d failed for qname %s !\n", pos, this->incluBegPosition + (uvc1_refgpos_t)(idx2symbol2data.size()), (NULL != bam ? bam_get_qname(bam) : "?")));
return this->idx2symbol2data[pos2];
};
uvc1_refgpos_t // size_t
getIncluBegPosition() const {
return this->incluBegPosition;
};
uvc1_refgpos_t // size_t
getExcluEndPosition() const {
return this->incluBegPosition + UNSIGN2SIGN(idx2symbol2data.size());
};
const std::map<uvc1_refgpos_t, std::map<uvc1_refgpos_t , uvc1_readnum_t>> &
getPosToDlenToData(const AlignmentSymbol s) const {
int idx = (LINK_D1 == s ? 0 : ((LINK_D2 == s) ? 1: 2));
return pos2dlen2data[idx];
};
const std::map<uvc1_refgpos_t, std::map<std::string, uvc1_readnum_t>> &
getPosToIseqToData(const AlignmentSymbol s) const {
int idx = (LINK_I1 == s ? 0 : ((LINK_I2 == s) ? 1: 2));
return pos2iseq2data[idx];
};
std::map<uvc1_refgpos_t, std::map<uvc1_readpos_t , uvc1_readnum_t>> &
getRefPosToDlenToData(const AlignmentSymbol s) {
int idx = (LINK_D1 == s ? 0 : ((LINK_D2 == s) ? 1: 2));
return pos2dlen2data[idx];
};
std::map<uvc1_refgpos_t, std::map<std::string, uvc1_refgpos_t>> &
getRefPosToIseqToData(const AlignmentSymbol s) {
int idx = (LINK_I1 == s ? 0 : ((LINK_I2 == s) ? 1: 2));
return pos2iseq2data[idx];
};
const ConsensusBlockSet &
getConsensusBlockSet(const ConsensusBlockCigarType cigar_type) const {
return conblocksets[cigar_type];
};
ConsensusBlockSet &
getRefConsensusBlockSet(const ConsensusBlockCigarType cigar_type) {
return conblocksets[cigar_type];
};
};
template <class TSymbol2Bucket2Count>
class GenericSymbol2Bucket2CountCoverage : public CoveredRegion<TSymbol2Bucket2Count> {
public:
GenericSymbol2Bucket2CountCoverage() : CoveredRegion<TSymbol2Bucket2Count>(0, 0, 1) { }
template <class T1, class T2, class T3>
GenericSymbol2Bucket2CountCoverage(T1 tid, T2 beg, T3 end) : CoveredRegion<TSymbol2Bucket2Count>(tid, beg, end) {}
};
typedef std::array<molcount_t, NUM_BUCKETS> Bucket2Count;
typedef GenericSymbol2Bucket2Count<Bucket2Count> Symbol2Bucket2Count;
typedef GenericSymbol2Count<uvc1_readnum_t> Symbol2Count;
typedef GenericSymbol2Bucket2CountCoverage<Symbol2Bucket2Count> Symbol2Bucket2CountCoverage;
typedef CoveredRegion<SegFormatPrepSet> SegFormatPrepSets;
typedef CoveredRegion<SegFormatThresSet> SegFormatThresSets;
typedef CoveredRegion<std::array<SegFormatInfoSet, NUM_ALIGNMENT_SYMBOLS>> Symbol2SegFormatInfoSets;
typedef CoveredRegion<std::array<FamFormatInfoSet, NUM_ALIGNMENT_SYMBOLS>> Symbol2FamFormatInfoSets;
typedef CoveredRegion<std::array<std::array<molcount_t, NUM_FRAG_FORMAT_DEPTH_SETS>, NUM_ALIGNMENT_SYMBOLS>> Symbol2FragFormatDepthSets;
typedef CoveredRegion<std::array<std::array<molcount_t, NUM_FAM_FORMAT_DEPTH_SETS>, NUM_ALIGNMENT_SYMBOLS>> Symbol2FamFormatDepthSets;
typedef CoveredRegion<std::array<std::array<molcount_t, NUM_DUPLEX_FORMAT_DEPTH_SETS>, NUM_ALIGNMENT_SYMBOLS>> Symbol2DuplexFormatDepthSets;
typedef CoveredRegion<std::array<std::array<molcount_t, NUM_VQ_FORMAT_TAG_SETS>, NUM_ALIGNMENT_SYMBOLS>> Symbol2VQFormatTagSets;
const size_t SIZE_PER_GENOMIC_POS = sizeof(SegFormatPrepSet)
+ sizeof(SegFormatThresSet)
+ ((sizeof(SegFormatInfoSet) + 2 * sizeof(FamFormatInfoSet)) * NUM_ALIGNMENT_SYMBOLS)
+ sizeof(molcount_t) * (NUM_FRAG_FORMAT_DEPTH_SETS + NUM_FAM_FORMAT_DEPTH_SETS * 2 + NUM_DUPLEX_FORMAT_DEPTH_SETS + NUM_VQ_FORMAT_TAG_SETS) * NUM_ALIGNMENT_SYMBOLS
+ NUM_BUCKETS;
template <class T1, class T2, class T3>
int
formatSumBySymbolType(
const T1 & xFormatYSets,
const T2 symboltype,
const T3 formatSet) {
int ret = 0;
for (const auto symbol : SYMBOL_TYPE_TO_SYMBOLS[symboltype]) {
ret += xFormatYSets[symbol][formatSet];
}
return ret;
};
void
initTidBegEnd(uvc1_refgpos_t & tid, uvc1_refgpos_t & inc_beg, uvc1_refgpos_t & exc_end) {
tid = -1;
inc_beg = INT32_MAX;
exc_end = 0;
};
int
fillTidBegEndFromAlns1(uvc1_refgpos_t & tid, uvc1_refgpos_t & inc_beg, uvc1_refgpos_t & exc_end, const std::vector<bam1_t *> & alns1, bool initialized=false) {
assertUVC(alns1.size() > 0);
if (!initialized) {
initTidBegEnd(tid, inc_beg, exc_end);
}
for (const bam1_t *aln : alns1) {
assertUVC (tid == -1 || SIGN2UNSIGN(aln->core.tid) == tid);
tid = aln->core.tid;
inc_beg = MIN(inc_beg, SIGN2UNSIGN(aln->core.pos));
exc_end = MAX(exc_end, SIGN2UNSIGN(bam_endpos(aln))) + 1; // The plus one accounts for possible insertion and/or soft-clip at the end
}
assertUVC (tid != -1);
assertUVC (inc_beg < exc_end);
return 0;
};
int
fillTidBegEndFromAlns2(uvc1_refgpos_t & tid, uvc1_refgpos_t & inc_beg, uvc1_refgpos_t & exc_end, const std::vector<std::vector<bam1_t *>> &alns2, bool initialized=false) {
assertUVC(alns2.size() > 0);
if (!initialized) {
initTidBegEnd(tid, inc_beg, exc_end);
}
for (auto alns1 : alns2) {
fillTidBegEndFromAlns1(tid, inc_beg, exc_end, alns1, true);
}
return 0;
};
int
fillTidBegEndFromAlns3(uvc1_refgpos_t & tid, uvc1_refgpos_t & inc_beg, uvc1_refgpos_t & exc_end, const std::vector<std::vector<std::vector<bam1_t *>>> & alns3, bool initialized=false) {
assertUVC(alns3.size() > 0);
if (!initialized) {
initTidBegEnd(tid, inc_beg, exc_end);
}
for (auto alns2 : alns3) {
fillTidBegEndFromAlns2(tid, inc_beg, exc_end, alns2, true);
}
return 0;
};
template <class T>
bool
is_indel_context_more_STR(uvc1_refgpos_t rulen1, uvc1_refgpos_t rc1, uvc1_refgpos_t rulen2, uvc1_refgpos_t rc2, const T indel_str_repeatsize_max) {
if (rulen2 * rc2 == 0) {
return true;
}
if (rulen1 > indel_str_repeatsize_max || rulen2 > indel_str_repeatsize_max) {
return ((rulen1 < rulen2 || (rulen1 == rulen2 && rc1 > rc2)) ? true : false);
}
int rank1 = (rc1 <= 1 ? (-(int)rc1 * rulen1) : ((int)(rc1 - 1) * rulen1));
int rank2 = (rc2 <= 1 ? (-(int)rc2 * rulen1) : ((int)(rc2 - 1) * rulen2));
if (0 == rc1 || 0 == rulen1) {
rank1 = -100;
}
if (0 == rc2 || 0 == rulen2) {
rank2 = -100;
}
if (rank1 > rank2) {
return true;
} else {
return false;
}
}
template <class T1, class T2, class T3>
uvc1_refgpos_t
indelpos_repeatsize_to_repeatnum(const T1 & refstring, const T2 refpos, const T3 repeatsize) {
uvc1_refgpos_t qidx = refpos;
while ((qidx + repeatsize < UNSIGN2SIGN(refstring.size())) && refstring[qidx] == refstring[qidx+repeatsize]) {
qidx++;
}
return (qidx - refpos) / repeatsize + 1;
}
int
indelpos_to_context(
std::string & repeatunit,
uvc1_refgpos_t & max_repeatnum,
const std::string & refstring,
uvc1_refgpos_t refpos,
uvc1_refgpos_t indel_str_repeatsize_max) {
max_repeatnum = 0;
if (refpos >= UNSIGN2SIGN(refstring.size())) {
repeatunit = "";
return -1;
}
uvc1_refgpos_t repeatsize_at_max_repeatnum = 0;
for (uvc1_refgpos_t repeatsize = 1; repeatsize <= indel_str_repeatsize_max; repeatsize++) {
uvc1_refgpos_t repeatnum = indelpos_repeatsize_to_repeatnum(refstring, refpos, repeatsize);
if (is_indel_context_more_STR(repeatsize, repeatnum, repeatsize_at_max_repeatnum, max_repeatnum, indel_str_repeatsize_max)) {
max_repeatnum = repeatnum;
repeatsize_at_max_repeatnum = repeatsize;
}
}
repeatunit = refstring.substr(refpos, repeatsize_at_max_repeatnum);
return 0;
}
uvc1_qual_t
indel_len_rusize_phred(uvc1_refgpos_t indel_len, uvc1_refgpos_t repeatunit_size) {
assertUVC (indel_len > 0 && repeatunit_size > 0);
// https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734402/#bib41 suggests power law with exponent of 1.5-1.6
// TODO: investigate this
// derived from the python code: for i in range(1, 20): print("{} {}".format( int( round(10.0/log(10.0)*log(i)) ) , i ))
const std::array<uvc1_qual_t, 18+1> n_units_to_phred = {{
0 ,
0 , // 1
3 , // 2
5 , // 3
6 , // 4
7 , // 5
8 , // 6
8 , // 7
9 , // 8
10 , // 9
10 , // 10
10 , // 11
11 , // 12
11 , // 13
11 , // 14
12 , // 15
12 , // 16
12 , // 17
13 , // 18
}};
if (0 == (indel_len % repeatunit_size)) {
auto n_units = indel_len / repeatunit_size;
return n_units_to_phred[MIN(n_units , UNSIGN2SIGN(n_units_to_phred.size()-1))];
} else {
return n_units_to_phred[MIN(indel_len, UNSIGN2SIGN(n_units_to_phred.size()-1))];
}
}
// https://www.ncbi.nlm.nih.gov/pmc/articles/PMC149199/ for artifactual errors
// https://www.cell.com/trends/genetics/fulltext/S0168-9525(13)00070-X, ref12, for germline variants
uvc1_qual_t
indel_phred(double ampfact, uvc1_refgpos_t repeatsize_at_max_repeatnum, uvc1_refgpos_t max_repeatnum) {
uvc1_refgpos_t region_size = repeatsize_at_max_repeatnum * max_repeatnum;
double num_slips = (region_size > 64 ? (double)(region_size - 8) : log1p(exp((double)region_size - (double)8)))
* ampfact / ((double)(repeatsize_at_max_repeatnum * repeatsize_at_max_repeatnum));
return prob2phred((1.0 - DBL_EPSILON) / (num_slips + 1.0));
// e.g. for the short tandem repeat ACACAC : repeatsize_at_max_repeatnum = 2, indel_n_units = 3, repeatunit = AC
}
std::vector<RegionalTandemRepeat>
refstring2repeatvec(
const std::string & refstring,
const uvc1_refgpos_t indel_str_repeatsize_max,
const uvc1_refgpos_t indel_minisattelite_repeatsize_max,
const uvc1_qual_t indel_BQ_max,
const double indel_polymerase_slip_rate,
const double indel_del_to_ins_err_ratio,
const uvc1_flag_t specialflag IGNORE_UNUSED_PARAM) {
std::vector<RegionalTandemRepeat> region_repeatvec(refstring.size());
for (auto & rtr : region_repeatvec) {
rtr.indelphred = indel_BQ_max;
}
for (uvc1_refgpos_t refpos = 0; refpos < UNSIGN2SIGN(refstring.size());) {
uvc1_refgpos_t repeatsize_at_max_repeatnum = 0;
uvc1_refgpos_t max_repeatnum = 0;
uvc1_refgpos_t repeat_endpos = refpos;
uvc1_refgpos_t anyTR_repeatsize_at_max_repeatnum = 0;
uvc1_refgpos_t anyTR_max_repeatnum = 0;
uvc1_refgpos_t anyTR_repeat_endpos = refpos;
for (uvc1_refgpos_t repeatsize = 1; repeatsize <= indel_minisattelite_repeatsize_max; repeatsize++) {
uvc1_refgpos_t qidx = refpos;
while (qidx + repeatsize < UNSIGN2SIGN(refstring.size()) && refstring[qidx] == refstring[qidx+repeatsize]) {
qidx++;
}
uvc1_refgpos_t repeatnum = (qidx - refpos) / repeatsize + 1;
if (repeatsize <= indel_str_repeatsize_max
&& is_indel_context_more_STR(repeatsize, repeatnum, repeatsize_at_max_repeatnum, max_repeatnum, indel_str_repeatsize_max)) {
repeatsize_at_max_repeatnum = repeatsize;
max_repeatnum = repeatnum;
repeat_endpos = qidx + repeatsize;
}
if (is_indel_context_more_STR(repeatsize, repeatnum, anyTR_repeatsize_at_max_repeatnum, anyTR_max_repeatnum, indel_minisattelite_repeatsize_max)) {
anyTR_repeatsize_at_max_repeatnum = repeatsize;
anyTR_max_repeatnum = repeatnum;
anyTR_repeat_endpos = qidx + repeatsize;
}
}
assertUVC(repeat_endpos > refpos);
{
uvc1_refgpos_t tl = MIN(repeat_endpos, UNSIGN2SIGN(refstring.size())) - refpos;
const uvc1_qual_t decphred = indel_phred(indel_polymerase_slip_rate * (indel_del_to_ins_err_ratio),
repeatsize_at_max_repeatnum, tl / repeatsize_at_max_repeatnum);
for (uvc1_refgpos_t i = refpos; i != MIN(repeat_endpos, UNSIGN2SIGN(refstring.size())); i++) {
if (tl > region_repeatvec[i].tracklen) {
region_repeatvec[i].begpos = refpos;
region_repeatvec[i].tracklen = tl;
region_repeatvec[i].unitlen = repeatsize_at_max_repeatnum;
region_repeatvec[i].indelphred = indel_BQ_max - MIN(indel_BQ_max - 1, decphred);
}
}
}
{
uvc1_refgpos_t anyTR_tl = MIN(anyTR_repeat_endpos, UNSIGN2SIGN(refstring.size())) - refpos;
for (uvc1_refgpos_t i = refpos; i != MIN(anyTR_repeat_endpos, UNSIGN2SIGN(refstring.size())); i++) {
if (anyTR_tl > region_repeatvec[i].anyTR_tracklen) {
region_repeatvec[i].anyTR_begpos = refpos;
region_repeatvec[i].anyTR_tracklen = anyTR_tl;
region_repeatvec[i].anyTR_unitlen = anyTR_repeatsize_at_max_repeatnum;
}
}
}
const auto nbases_to_next = indel_str_repeatsize_max + repeatsize_at_max_repeatnum;
refpos += MAX(repeatsize_at_max_repeatnum * max_repeatnum, nbases_to_next + 1) - (nbases_to_next);
}
region_repeatvec.push_back(LAST(region_repeatvec));
return region_repeatvec;
}
template <class T1, class T2>
uvc1_qual_t
ref_to_phredvalue(uvc1_refgpos_t & n_units,
uvc1_refgpos_t & max_repeatnum,
uvc1_refgpos_t & repeatsize_at_max_repeatnum,
const T1 & refstring,
const uvc1_refgpos_t refpos,
const uvc1_qual_t max_phred,
double ampfact,
const uvc1_refgpos_t cigar_oplen,
const T2 cigar_op,
const uvc1_refgpos_t indel_str_repeatsize_max,
const double indel_del_to_ins_err_ratio,
const uvc1_flag_t specialflag IGNORE_UNUSED_PARAM) {
max_repeatnum = 0;
repeatsize_at_max_repeatnum = 0;
for (uvc1_refgpos_t repeatsize = 1; repeatsize <= indel_str_repeatsize_max; repeatsize++) {
uvc1_refgpos_t qidx = refpos;
while (qidx + repeatsize < UNSIGN2SIGN(refstring.size()) && refstring[qidx] == refstring[qidx+repeatsize]) {
qidx++;
}
uvc1_refgpos_t repeatnum = (qidx - refpos) / repeatsize + 1;
if (is_indel_context_more_STR(repeatsize, repeatnum, repeatsize_at_max_repeatnum, max_repeatnum, indel_str_repeatsize_max)) {
max_repeatnum = repeatnum;
repeatsize_at_max_repeatnum = repeatsize;
}
}
if (cigar_oplen == repeatsize_at_max_repeatnum && cigar_op == BAM_CDEL) {
ampfact *= indel_del_to_ins_err_ratio;
}
// Because of a higher number of PCR cycles, it is higher than the one set in Fig. 3 at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC149199/
uvc1_qual_t decphred = indel_phred(ampfact, repeatsize_at_max_repeatnum, max_repeatnum);
if (0x1 == (specialflag & 0x1)) {
LOG(logINFO) << "indel_phred("
<< ampfact << ", "
<< repeatsize_at_max_repeatnum << ", "
<< max_repeatnum << ") = " << decphred;
}
// The number of units should minimize InDel collision.
if (repeatsize_at_max_repeatnum * (max_repeatnum - 1) >= 6 - 1) {
n_units = ((0 == cigar_oplen % repeatsize_at_max_repeatnum) ? (cigar_oplen / repeatsize_at_max_repeatnum) : ((1 == cigar_oplen) ? 1 : 0));
} else {
n_units = 1 + (cigar_oplen / 6);
}
return max_phred - MIN(max_phred, decphred) + indel_len_rusize_phred(cigar_oplen, repeatsize_at_max_repeatnum);
}
int
update_seg_format_prep_sets_by_aln(
SegFormatPrepSets & seg_format_prep_sets,
const bam1_t *aln,
const std::vector<RegionalTandemRepeat> & rtr_vec,
const CoveredRegion<uvc1_qual_big_t> & baq_offsetarr,
const uvc1_refgpos_t region_offset,
const uvc1_flag_t dflag,
const std::basic_string<AlignmentSymbol> & region_symbolvec,
const CommandLineArgs & paramset,
const uvc1_flag_t specialflag IGNORE_UNUSED_PARAM) {
const uvc1_refgpos_t rend = bam_endpos(aln);
const auto cigar = bam_get_cigar(aln);
uvc1_refgpos_t nge_cnt = 0; // number of gap extensions.
uvc1_refgpos_t ngo_cnt = 0; // number of gap openings.
uvc1_qual_t insbaq_sum = 0;
uvc1_qual_t delbaq_sum = 0;
uvc1_readpos_t inslen_sum = 0;
uvc1_readpos_t dellen_sum = 0;
uvc1_refgpos_t qpos = 0;
uvc1_refgpos_t rpos = aln->core.pos;
uvc1_readpos_t max_clip_len = 0;
uvc1_readpos_t max_indel_len = 0;
for (uint32_t i = 0; i < aln->core.n_cigar; i++) {
const auto c = cigar[i];
const auto cigar_op = bam_cigar_op(c);
const auto cigar_oplen = bam_cigar_oplen(c);
if (BAM_CINS == cigar_op || BAM_CDEL == cigar_op) {
nge_cnt += bam_cigar_oplen(c);
ngo_cnt++;
if (BAM_CINS == cigar_op) {
insbaq_sum += baq_offsetarr.getByPos(MIN(rpos + UNSIGN2SIGN(cigar_oplen), baq_offsetarr.getExcluEndPosition() - 1)) - baq_offsetarr.getByPos(rpos);
inslen_sum += bam_cigar_oplen(c);
qpos += cigar_oplen;
} else if (BAM_CDEL == cigar_op) {
delbaq_sum += baq_offsetarr.getByPos(MIN(rpos + UNSIGN2SIGN(cigar_oplen), baq_offsetarr.getExcluEndPosition() - 1)) - baq_offsetarr.getByPos(rpos);
dellen_sum += bam_cigar_oplen(c);
rpos += cigar_oplen;
}
} else if (cigar_op == BAM_CMATCH || cigar_op == BAM_CEQUAL || cigar_op == BAM_CDIFF) {
UPDATE_MAX(max_indel_len, UNSIGN2SIGN(cigar_oplen));
qpos += cigar_oplen;
rpos += cigar_oplen;
} else {
if (cigar_op == BAM_CSOFT_CLIP || cigar_op == BAM_CHARD_CLIP) {
UPDATE_MAX(max_clip_len, UNSIGN2SIGN(cigar_oplen));
}
process_cigar(qpos, rpos, cigar_op, cigar_oplen);
}
}
const auto *bam_aux_data = bam_aux_get(aln, "NM");
const uvc1_refgpos_t nm_cnt = ((bam_aux_data != NULL) ? bam_aux2i(bam_aux_data) : nge_cnt);
assertUVC (nm_cnt >= nge_cnt);
const uvc1_base1500x_t xm_cnt = nm_cnt - nge_cnt;
const uvc1_base1500x_t xm1500 = xm_cnt * 1500 / (rend - aln->core.pos);
const uvc1_base1500x_t go1500 = ngo_cnt * 1500 / (rend - aln->core.pos);
const uvc1_base1500x_t avg_gaplen = nge_cnt / MAX(1, ngo_cnt);
const uvc1_refgpos_t frag_pos_L = MIN(aln->core.pos, aln->core.mpos);
const uvc1_refgpos_t frag_pos_R = (frag_pos_L + abs(aln->core.isize));
const bool isrc = ((aln->core.flag & 0x10) == 0x10);
// strand does not seem to be useful here?
/*
const bool isr2 = ((aln->core.flag & 0x80) == 0x80 && (aln->core.flag & 0x1) == 0x1);
const bool strand = bam_get_strand(aln); //(isrc ^ isr2);
*/
const auto pcr_dp_inc = ((dflag & 0x4) ? 1 : 0);
const auto umi_dp_inc = ((dflag & 0x1) ? 1 : 0);
qpos = 0;
rpos = aln->core.pos;