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blight.cpp
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blight.cpp
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#include "blight.h"
#include "include/bbhash.h"
#include "include/common.h"
#include "lz4/lz4_stream.h"
#include "include/robin_hood.h"
#include "utils.h"
#include "include/zstr.hpp"
#include <algorithm>
#include <atomic>
#include <chrono>
#include <fstream>
#include <iostream>
#include <map>
#include <math.h>
#include <mutex>
#include <omp.h>
#include <pthread.h>
#include <stdint.h>
#include <stdio.h>
#include <sys/stat.h>
#include <tmmintrin.h>
#include <unistd.h>
#include <unordered_map>
#include <vector>
using namespace std;
using namespace chrono;
uint64_t kmer_Set_Light::get_kmer_number(){
return number_kmer;
}
__uint128_t kmer_Set_Light::rcb(const __uint128_t& in) {
assume(k <= 64, "k=%u > 64", k);
union kmer_u {
__uint128_t k;
__m128i m128i;
uint64_t u64[2];
uint8_t u8[16];
};
kmer_u res = {.k = in};
static_assert(sizeof(res) == sizeof(__uint128_t), "kmer sizeof mismatch");
// Swap byte order
kmer_u shuffidunrevhash = {.u8 = {15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0}};
res.m128i = _mm_shuffle_epi8(res.m128i, shuffidunrevhash.m128i);
// Swap nuc order in bytes
const uint64_t c1 = 0x0f0f0f0f0f0f0f0f;
const uint64_t c2 = 0x3333333333333333;
for (uint64_t& x : res.u64) {
x = ((x & c1) << 4) | ((x & (c1 << 4)) >> 4); // swap 2-nuc order in bytes
x = ((x & c2) << 2) | ((x & (c2 << 2)) >> 2); // swap nuc order in 2-nuc
x ^= 0xaaaaaaaaaaaaaaaa; // Complement;
}
// Realign to the right
res.m128i = mm_bitshift_right(res.m128i, 128 - 2 * k);
return res.k;
}
uint64_t kmer_Set_Light::rcb(const uint64_t& in) {
assume(k <= 32, "k=%u > 32", k);
// Complement, swap byte order
uint64_t res = __builtin_bswap64(in ^ 0xaaaaaaaaaaaaaaaa);
// Swap nuc order in bytes
const uint64_t c1 = 0x0f0f0f0f0f0f0f0f;
const uint64_t c2 = 0x3333333333333333;
res = ((res & c1) << 4) | ((res & (c1 << 4)) >> 4); // swap 2-nuc order in bytes
res = ((res & c2) << 2) | ((res & (c2 << 2)) >> 2); // swap nuc order in 2-nuc
// Realign to the right
res >>= 64 - 2 * k;
return res;
}
uint64_t kmer_Set_Light::canonize(uint64_t x, uint64_t n) {
return min(x, rcbc(x, n));
}
void kmer_Set_Light::updateK(kmer& min, char nuc) {
min <<= 2;
min += nuc2int(nuc);
min %= offsetUpdateAnchor;
}
void kmer_Set_Light::updateM(kmer& min, char nuc) {
min <<= 2;
min += nuc2int(nuc);
min %= offsetUpdateMinimizer;
}
void kmer_Set_Light::updateRCK(kmer& min, char nuc) {
min >>= 2;
min += (nuc2intrc(nuc) << (2 * k - 2));
}
void kmer_Set_Light::updateRCM(kmer& min, char nuc) {
min >>= 2;
min += (nuc2intrc(nuc) << (2 * minimizer_size_graph - 2));
}
kmer get_int_in_kmer(kmer seq, uint64_t pos, uint64_t number_nuc) {
seq >>= 2 * pos;
return ((seq) % (1 << (2 * number_nuc)));
}
kmer kmer_Set_Light::regular_minimizer(kmer seq) {
kmer mini, mmer;
mmer = seq % minimizer_number_graph;
mini = mmer = canonize(mmer, minimizer_size_graph);
uint64_t hash_mini = (unrevhash(mmer));
for (uint64_t i(1); i <= k - minimizer_size_graph; i++) {
seq >>= 2;
mmer = seq % minimizer_number_graph;
mmer = canonize(mmer, minimizer_size_graph);
uint64_t hash = (unrevhash(mmer));
if (hash_mini > hash) {
mini = mmer;
hash_mini = hash;
}
}
return revhash((uint64_t)mini) % minimizer_number;
}
kmer kmer_Set_Light::regular_minimizer_pos(kmer seq, uint64_t& position) {
kmer mini, mmer;
mmer = seq % minimizer_number_graph;
mini = mmer = canonize(mmer, minimizer_size_graph);
uint64_t hash_mini = (unrevhash(mmer));
position = 0;
for (uint64_t i(1); i <= k - minimizer_size_graph; i++) {
seq >>= 2;
mmer = seq % minimizer_number_graph;
mmer = canonize(mmer, minimizer_size_graph);
uint64_t hash = (unrevhash(mmer));
if (hash_mini > hash) {
position = k - minimizer_size_graph - i;
mini = mmer;
hash_mini = hash;
}
}
return mini;
}
void kmer_Set_Light::construct_index(const string& input_file, const string& tmp_dir) {
if (not tmp_dir.empty()) {
working_dir = tmp_dir + "/";
}
if (m1 < m2) {
cout << "n should be inferior to m" << endl;
exit(0);
}
high_resolution_clock::time_point t1 = high_resolution_clock::now();
nuc_minimizer = new uint32_t[minimizer_number.value()];
current_pos = new uint64_t[minimizer_number.value()];
start_bucket = new uint64_t[minimizer_number.value()];
create_super_buckets(input_file);
high_resolution_clock::time_point t12 = high_resolution_clock::now();
duration<double> time_span12 = duration_cast<duration<double> >(t12 - t1);
cout << "Super bucket created: " << time_span12.count() << " seconds." << endl;
read_super_buckets(working_dir + "_blout");
high_resolution_clock::time_point t13 = high_resolution_clock::now();
duration<double> time_span13 = duration_cast<duration<double> >(t13 - t12);
cout << "Indexes created: " << time_span13.count() << " seconds." << endl;
duration<double> time_spant = duration_cast<duration<double> >(t13 - t1);
cout << "The whole indexing took me " << time_spant.count() << " seconds." << endl;
delete[] nuc_minimizer;
delete[] start_bucket;
delete[] current_pos;
}
void kmer_Set_Light::reset() {
number_kmer = number_super_kmer = largest_MPHF = positions_total_size = positions_int = total_nb_minitigs = largest_bucket_nuc_all = 0;
for (uint64_t i(0); i < mphf_number; ++i) {
all_mphf[i].mphf_size = 0;
all_mphf[i].bit_to_encode = 0;
all_mphf[i].start = 0;
all_mphf[i].empty = true;
}
for (uint64_t i(0); i < minimizer_number.value(); ++i) {
//all_buckets[i].start=0;
nuc_minimizer[i] = 0;
start_bucket[i] = 0;
current_pos[i] = 0;
all_buckets[i].skmer_number = 0;
}
}
string kmer_Set_Light::compaction(const string& seq1, const string& seq2, bool recur = true) {
uint s1(seq1.size()), s2(seq2.size());
if (s1 == 0 or s2 == 0) {
return "";
}
string rc2(revComp(seq2)), end1(seq1.substr(s1 - k + 1, k - 1)), beg2(seq2.substr(0, k - 1));
if (end1 == beg2) {
return seq1 + (seq2.substr(k - 1));
}
string begrc2(rc2.substr(0, k - 1));
if (end1 == begrc2) {
return seq1 + (rc2.substr(k - 1));
}
if (recur) {
return compaction(revComp(seq1), seq2, false);
} else {
}
return "";
}
void kmer_Set_Light::create_super_buckets(const string& input_file) {
struct rlimit rl;
getrlimit(RLIMIT_NOFILE, &rl);
rl.rlim_cur = number_superbuckets.value() + 10;
setrlimit(RLIMIT_NOFILE, &rl);
uint64_t total_nuc_number(0);
istream* inUnitigs;
bool is_gzip_compressed = input_file.substr(input_file.length() - 2) == "gz";
if (is_gzip_compressed)
inUnitigs = new zstr::ifstream(input_file);
else
inUnitigs = new lz4_stream::istream(input_file);
if (not inUnitigs->good()) {
cout << "Problem with files opening" << endl;
exit(1);
}
vector<ostream*> out_files;
for (uint64_t i(0); i < number_superbuckets; ++i) {
auto out = new zstr::ofstream(working_dir + "_blout" + to_string(i) + ".gz");
if (not out->good()) {
cout << "Problem with files opening" << endl;
exit(1);
}
out_files.push_back(out);
}
omp_lock_t lock[number_superbuckets.value()];
for (uint64_t i = 0; i < number_superbuckets; i++) {
omp_init_lock(&(lock[i]));
}
#pragma omp parallel num_threads(coreNumber)
{
string ref, useless;
vector<string> buffer(number_superbuckets.value());
minimizer_type old_minimizer, minimizer;
while (not inUnitigs->eof()) {
ref = useless = "";
#pragma omp critical(dataupdate)
{
getline(*inUnitigs, useless);
getline(*inUnitigs, ref);
if (ref.size() < k) {
ref = "";
} else {
read_kmer += ref.size() - k + 1;
}
}
// FOREACH UNITIG
if (not ref.empty() and not useless.empty()) {
old_minimizer = minimizer = minimizer_number.value();
uint64_t last_position(0);
// FOREACH KMER
kmer seq(str2num(ref.substr(0, k)));
uint64_t position_min;
kmer min_seq = (str2num(ref.substr(k - minimizer_size_graph, minimizer_size_graph))), min_rcseq(rcbc(min_seq, minimizer_size_graph)),
min_canon(min(min_seq, min_rcseq));
minimizer = regular_minimizer_pos(seq, position_min);
old_minimizer = minimizer;
uint64_t hash_min = unrevhash(minimizer);
uint64_t i(0);
for (; i + k < ref.size(); ++i) {
updateK(seq, ref[i + k]);
updateM(min_seq, ref[i + k]);
updateRCM(min_rcseq, ref[i + k]);
min_canon = (min(min_seq, min_rcseq));
uint64_t new_h = unrevhash(min_canon);
// THE NEW mmer is a MINIMIZor
if (new_h < hash_min) {
minimizer = (min_canon);
hash_min = new_h;
position_min = i + k - minimizer_size_graph + 1;
} else {
// the previous minimizer is outdated
if (i >= position_min) {
minimizer = regular_minimizer_pos(seq, position_min);
hash_min = unrevhash(minimizer);
position_min += (i + 1);
} else {
}
}
// COMPUTE KMER MINIMIZER
if (revhash(old_minimizer) % minimizer_number != revhash(minimizer) % minimizer_number) {
old_minimizer = (revhash(old_minimizer) % minimizer_number);
buffer[old_minimizer / bucket_per_superBuckets.value()] += ">" + to_string(old_minimizer) + "\n" + ref.substr(last_position, i - last_position + k) + "\n";
// *(out_files[((old_minimizer))/bucket_per_superBuckets])<<">"+to_string(old_minimizer)+"\n"<<ref.substr(last_position,i-last_position+k)<<"\n";
if (buffer[old_minimizer / bucket_per_superBuckets.value()].size() > 80000) {
omp_set_lock(&(lock[((old_minimizer)) / bucket_per_superBuckets.value()]));
*(out_files[((old_minimizer)) / bucket_per_superBuckets.value()]) << buffer[old_minimizer / bucket_per_superBuckets.value()];
omp_unset_lock(&(lock[((old_minimizer)) / bucket_per_superBuckets.value()]));
buffer[old_minimizer / bucket_per_superBuckets.value()].clear();
}
#pragma omp atomic
nuc_minimizer[old_minimizer] += (i - last_position + k);
#pragma omp atomic
all_buckets[old_minimizer].skmer_number++;
#pragma omp atomic
all_mphf[old_minimizer / number_bucket_per_mphf].mphf_size += (i - last_position + k) - k + 1;
all_mphf[old_minimizer / number_bucket_per_mphf].empty = false;
#pragma omp atomic
total_nuc_number += (i - last_position + k);
last_position = i + 1;
old_minimizer = minimizer;
}
}
if (ref.size() - last_position > k - 1) {
old_minimizer = (revhash(old_minimizer) % minimizer_number);
buffer[old_minimizer / bucket_per_superBuckets.value()] += ">" + to_string(old_minimizer) + "\n" + ref.substr(last_position) + "\n";
// *(out_files[((old_minimizer))/bucket_per_superBuckets])<<">"+to_string(old_minimizer)+"\n"<<ref.substr(last_position)<<"\n";
if (buffer[old_minimizer / bucket_per_superBuckets.value()].size() > 80000) {
omp_set_lock(&(lock[((old_minimizer)) / bucket_per_superBuckets.value()]));
*(out_files[((old_minimizer)) / bucket_per_superBuckets.value()]) << buffer[old_minimizer / bucket_per_superBuckets.value()];
omp_unset_lock(&(lock[((old_minimizer)) / bucket_per_superBuckets.value()]));
buffer[old_minimizer / bucket_per_superBuckets.value()].clear();
}
#pragma omp atomic
nuc_minimizer[old_minimizer] += (ref.substr(last_position)).size();
#pragma omp atomic
all_buckets[old_minimizer].skmer_number++;
#pragma omp atomic
total_nuc_number += (ref.substr(last_position)).size();
#pragma omp atomic
all_mphf[old_minimizer / number_bucket_per_mphf].mphf_size += (ref.substr(last_position)).size() - k + 1;
all_mphf[old_minimizer / number_bucket_per_mphf].empty = false;
}
}
}
for (uint64_t i(0); i < number_superbuckets.value(); ++i) {
if (not buffer[i].empty()) {
omp_set_lock(&(lock[i]));
*(out_files[i]) << buffer[i];
omp_unset_lock(&(lock[i]));
}
}
}
delete inUnitigs;
for (uint64_t i(0); i < number_superbuckets; ++i) {
*out_files[i] << flush;
delete (out_files[i]);
}
bucketSeq.resize(total_nuc_number * 2);
bucketSeq.shrink_to_fit();
uint64_t i(0), total_pos_size(0);
uint32_t max_bucket_mphf(0);
uint64_t hash_base(0), old_hash_base(0), nb_skmer_before(0), last_skmer_number(0);
for (uint64_t BC(0); BC < minimizer_number.value(); ++BC) {
start_bucket[BC] = i;
current_pos[BC] = i;
i += nuc_minimizer[BC];
max_bucket_mphf = max(all_buckets[BC].skmer_number, max_bucket_mphf);
if (BC == 0) {
nb_skmer_before = 0; // I replace skmer_number by the total number of minitigs before this bucket
} else {
nb_skmer_before = all_buckets[BC - 1].skmer_number;
}
uint64_t local_skmercount(all_buckets[BC].skmer_number);
all_buckets[BC].skmer_number = total_nb_minitigs;
total_nb_minitigs += local_skmercount;
if ((BC + 1) % number_bucket_per_mphf == 0) {
int n_bits_to_encode((ceil(log2(max_bucket_mphf + 1))) - bit_saved_sub);
if (n_bits_to_encode < 1) {
n_bits_to_encode = 1;
}
all_mphf[BC / number_bucket_per_mphf].bit_to_encode = n_bits_to_encode;
all_mphf[BC / number_bucket_per_mphf].start = total_pos_size;
total_pos_size += (n_bits_to_encode * all_mphf[BC / number_bucket_per_mphf].mphf_size);
hash_base += all_mphf[(BC / number_bucket_per_mphf)].mphf_size;
all_mphf[BC / number_bucket_per_mphf].mphf_size = old_hash_base;
old_hash_base = hash_base;
max_bucket_mphf = 0;
}
}
total_nb_minitigs = all_buckets[(uint)minimizer_number - 1].skmer_number + last_skmer_number; // total number of minitigs
positions.resize(total_pos_size);
positions_int = positions.size() / 64 + (positions.size() % 64 == 0 ? 0 : 1);
positions.shrink_to_fit();
// initialize_buckets();
}
void kmer_Set_Light::initialize_buckets() {
bucketSeq.resize(total_nuc_number * 2);
bucketSeq.shrink_to_fit();
uint64_t i(0), total_pos_size(0);
uint32_t max_bucket_mphf(0);
uint64_t hash_base(0), old_hash_base(0), nb_skmer_before(0), last_skmer_number(0);
for (uint64_t BC(0); BC < minimizer_number.value(); ++BC) {
start_bucket[BC] = i;
current_pos[BC] = i;
i += nuc_minimizer[BC];
max_bucket_mphf = max(all_buckets[BC].skmer_number, max_bucket_mphf);
if (BC == 0) {
nb_skmer_before = 0; // I replace skmer_number by the total number of minitigs before this bucket
} else {
nb_skmer_before = all_buckets[BC - 1].skmer_number;
}
uint64_t local_skmercount(all_buckets[BC].skmer_number);
all_buckets[BC].skmer_number = total_nb_minitigs;
total_nb_minitigs += local_skmercount;
if ((BC + 1) % number_bucket_per_mphf == 0) {
int n_bits_to_encode((ceil(log2(max_bucket_mphf + 1))) - bit_saved_sub);
if (n_bits_to_encode < 1) {
n_bits_to_encode = 1;
}
all_mphf[BC / number_bucket_per_mphf].bit_to_encode = n_bits_to_encode;
all_mphf[BC / number_bucket_per_mphf].start = total_pos_size;
total_pos_size += (n_bits_to_encode * all_mphf[BC / number_bucket_per_mphf].mphf_size);
hash_base += all_mphf[(BC / number_bucket_per_mphf)].mphf_size;
all_mphf[BC / number_bucket_per_mphf].mphf_size = old_hash_base;
old_hash_base = hash_base;
max_bucket_mphf = 0;
}
}
total_nb_minitigs = all_buckets[(uint)minimizer_number - 1].skmer_number + last_skmer_number; // total number of minitigs
positions.resize(total_pos_size);
positions_int = positions.size() / 64 + (positions.size() % 64 == 0 ? 0 : 1);
positions.shrink_to_fit();
}
void kmer_Set_Light::str2bool(const string& str, uint64_t mini) {
for (uint64_t i(0); i < str.size(); ++i) {
switch (str[i]) {
case 'A':
bucketSeq[(current_pos[mini] + i) * 2] = (false);
bucketSeq[(current_pos[mini] + i) * 2 + 1] = (false);
break;
case 'C':
bucketSeq[(current_pos[mini] + i) * 2] = (false);
bucketSeq[(current_pos[mini] + i) * 2 + 1] = (true);
break;
case 'G':
bucketSeq[(current_pos[mini] + i) * 2] = (true);
bucketSeq[(current_pos[mini] + i) * 2 + 1] = (true);
break;
default:
bucketSeq[(current_pos[mini] + i) * 2] = (true);
bucketSeq[(current_pos[mini] + i) * 2 + 1] = (false);
break;
}
}
current_pos[mini] += (str.size());
}
uint64_t kmer_Set_Light::get_minimizer_from_header(zstr::ifstream& in) {
unsigned compressed_header_size;
char c = in.get(); //read ">"
int32_t minimizer;
in.read(reinterpret_cast<char*>(&minimizer), sizeof(int32_t)); // minimizer_size
in.read(reinterpret_cast<char*>(&compressed_header_size), sizeof(unsigned)); // size of colors/counts with rle
unsigned char* comp; //todo optim
comp = new unsigned char[compressed_header_size + 1];
//~ in.seekg(compressed_header_size + 1, in.cur); // rle + \n
in.read((char*) comp, compressed_header_size + 1);
delete [] comp ;
return minimizer;
}
void kmer_Set_Light::read_super_buckets_reindeer(const string& input_file) {
#pragma omp parallel num_threads(coreNumber)
{
string header, line, mini;
bm::bvector<> position_super_kmers_local;
#pragma omp for
for (uint64_t SBC = 0; SBC < number_superbuckets.value(); ++SBC) {
position_super_kmers_local.init();
vector<uint64_t> number_kmer_accu(bucket_per_superBuckets.value(), 0);
uint64_t BC(SBC * bucket_per_superBuckets);
zstr::ifstream in((input_file + to_string(SBC) + ".gz"));
int32_t minimizer;
in.peek();
while (not in.eof() and in.good()) {
header = line = "";
minimizer = get_minimizer_from_header(in);
getline(in, line); //sequence
if (not line.empty()) {
str2bool(line, minimizer);
position_super_kmers_local[number_kmer_accu[minimizer % bucket_per_superBuckets] + all_mphf[minimizer].mphf_size] = true;
#pragma omp atomic
number_kmer += line.size() - k + 1;
number_kmer_accu[minimizer % bucket_per_superBuckets] += line.size() - k + 1;
#pragma omp atomic
++number_super_kmer;
line.clear();
}
in.peek();
}
create_mphf_disk(BC, BC + bucket_per_superBuckets, position_super_kmers_local);
fill_positions(BC, BC + bucket_per_superBuckets, position_super_kmers_local);
BC += bucket_per_superBuckets.value();
cout << "-" << flush;
}
#pragma omp critical(PSK)
{ position_super_kmers.merge(position_super_kmers_local); }
}
position_super_kmers[number_kmer] = true;
position_super_kmers.optimize();
position_super_kmers.optimize_gap_size();
position_super_kmers_RS = new bm::bvector<>::rs_index_type();
position_super_kmers.build_rs_index(position_super_kmers_RS);
cout << endl;
cout << "----------------------INDEX RECAP----------------------------" << endl;
cout << "Kmer in graph: " << intToString(number_kmer) << endl;
cout << "Super Kmer in graph: " << intToString(number_super_kmer) << endl;
cout << "Average size of Super Kmer: " << intToString(number_kmer / (number_super_kmer)) << endl;
cout << "Total size of the partitionned graph: " << intToString(bucketSeq.capacity() / 2) << endl;
cout << "Largest MPHF: " << intToString(largest_MPHF) << endl;
cout << "Largest Bucket: " << intToString(largest_bucket_nuc_all) << endl;
cout << "Size of the partitionned graph (MBytes): " << intToString(bucketSeq.size() / (8 * 1024 * 1024)) << endl;
cout << "Total Positions size (MBytes): " << intToString(positions.size() / (8 * 1024 * 1024)) << endl;
cout << "Size of the partitionned graph (bit per kmer): " << ((double)(bucketSeq.size()) / (number_kmer)) << endl;
bit_per_kmer += ((double)(bucketSeq.size()) / (number_kmer));
cout << "Total Positions size (bit per kmer): " << ((double)positions.size() / number_kmer) << endl;
bit_per_kmer += ((double)positions.size() / number_kmer);
cout << "TOTAL Bits per kmer (without bbhash): " << bit_per_kmer << endl;
cout << "TOTAL Bits per kmer (with bbhash): " << bit_per_kmer + 4 << endl;
cout << "TOTAL Size estimated (MBytes): " << (bit_per_kmer + 4) * number_kmer / (8 * 1024 * 1024) << endl;
}
void kmer_Set_Light::read_super_buckets(const string& input_file) {
#pragma omp parallel num_threads(coreNumber)
{
string useless, line;
bm::bvector<> position_super_kmers_local;
#pragma omp for
for (uint64_t SBC = 0; SBC < number_superbuckets.value(); ++SBC) {
position_super_kmers_local.init();
vector<uint64_t> number_kmer_accu(bucket_per_superBuckets.value(), 0);
uint64_t BC(SBC * bucket_per_superBuckets);
zstr::ifstream in((input_file + to_string(SBC) + ".gz"));
while (not in.eof() and in.good()) {
useless = line = "";
getline(in, useless);
getline(in, line);
if (not line.empty()) {
useless = useless.substr(1);
uint64_t minimizer(stoi(useless));
str2bool(line, minimizer);
position_super_kmers_local[number_kmer_accu[minimizer % bucket_per_superBuckets] + all_mphf[minimizer].mphf_size] = true;
#pragma omp atomic
number_kmer += line.size() - k + 1;
number_kmer_accu[minimizer % bucket_per_superBuckets] += line.size() - k + 1;
#pragma omp atomic
++number_super_kmer;
line.clear();
}
}
remove((input_file + to_string(SBC) + ".gz").c_str());
create_mphf_disk(BC, BC + bucket_per_superBuckets, position_super_kmers_local);
fill_positions(BC, BC + bucket_per_superBuckets, position_super_kmers_local);
BC += bucket_per_superBuckets.value();
cout << "-" << flush;
}
#pragma omp critical(PSK)
{ position_super_kmers.merge(position_super_kmers_local); }
}
position_super_kmers[number_kmer] = true;
position_super_kmers.optimize();
position_super_kmers.optimize_gap_size();
position_super_kmers_RS = new bm::bvector<>::rs_index_type();
position_super_kmers.build_rs_index(position_super_kmers_RS);
cout << endl;
cout << "----------------------INDEX RECAP----------------------------" << endl;
cout << "Kmer in graph: " << intToString(number_kmer) << endl;
cout << "Super Kmer in graph: " << intToString(number_super_kmer) << endl;
cout << "Average size of Super Kmer: " << intToString(number_kmer / (number_super_kmer)) << endl;
cout << "Total size of the partitionned graph: " << intToString(bucketSeq.capacity() / 2) << endl;
cout << "Largest MPHF: " << intToString(largest_MPHF) << endl;
cout << "Largest Bucket: " << intToString(largest_bucket_nuc_all) << endl;
cout << "Size of the partitionned graph (MBytes): " << intToString(bucketSeq.size() / (8 * 1024 * 1024)) << endl;
cout << "Total Positions size (MBytes): " << intToString(positions.size() / (8 * 1024 * 1024)) << endl;
cout << "Size of the partitionned graph (bit per kmer): " << ((double)(bucketSeq.size()) / (number_kmer)) << endl;
bit_per_kmer += ((double)(bucketSeq.size()) / (number_kmer));
cout << "Total Positions size (bit per kmer): " << ((double)positions.size() / number_kmer) << endl;
bit_per_kmer += ((double)positions.size() / number_kmer);
cout << "TOTAL Bits per kmer (without bbhash): " << bit_per_kmer << endl;
cout << "TOTAL Bits per kmer (with bbhash): " << bit_per_kmer + 4 << endl;
cout << "TOTAL Size estimated (MBytes): " << (bit_per_kmer + 4) * number_kmer / (8 * 1024 * 1024) << endl;
}
inline kmer kmer_Set_Light::get_kmer(uint64_t mini, uint64_t pos) {
kmer res(0);
uint64_t bit = (start_bucket[mini] + pos) * 2;
const uint64_t bitlast = bit + 2 * k;
for (; bit < bitlast; bit += 2) {
res <<= 2;
res |= bucketSeq[bit] * 2 | bucketSeq[bit + 1];
}
return res;
}
inline kmer kmer_Set_Light::get_kmer(uint64_t pos) {
kmer res(0);
uint64_t bit = (pos)*2;
const uint64_t bitlast = bit + 2 * k;
for (; bit < bitlast; bit += 2) {
res <<= 2;
res |= bucketSeq[bit] * 2 | bucketSeq[bit + 1];
}
return res;
}
inline kmer kmer_Set_Light::update_kmer(uint64_t pos, kmer mini, kmer input) {
return update_kmer_local(start_bucket[mini] + pos, bucketSeq, input);
}
inline kmer kmer_Set_Light::update_kmer_local(uint64_t pos, const vector<bool>& V, kmer input) {
input <<= 2;
uint64_t bit0 = pos * 2;
input |= V[bit0] * 2 | V[bit0 + 1];
return input % offsetUpdateAnchor;
}
void kmer_Set_Light::print_kmer(kmer num, uint64_t n) {
Pow2<kmer> anc(2 * (k - 1));
for (uint64_t i(0); i < k and i < n; ++i) {
uint64_t nuc = num / anc;
num = num % anc;
if (nuc == 2) {
cout << "T";
}
if (nuc == 3) {
cout << "G";
}
if (nuc == 1) {
cout << "C";
}
if (nuc == 0) {
cout << "A";
}
if (nuc >= 4) {
cout << nuc << endl;
cout << "WTF" << endl;
}
anc >>= 2;
}
cout << endl;
}
string kmer_Set_Light::kmer2str(kmer num) {
string res(k, '\0');
Pow2<kmer> anc(2 * (k - 1));
for (uint64_t i(0); i < k; ++i) {
uint64_t nuc = num / anc;
num = num % anc;
assert(nuc < 4);
res[i] = "ACTG"[nuc];
anc >>= 2;
}
return res;
}
void kmer_Set_Light::create_mphf_mem(uint64_t begin_BC, uint64_t end_BC) {
#pragma omp parallel num_threads(coreNumber)
{
vector<kmer> anchors;
uint32_t largest_bucket_anchor(0);
uint32_t largest_bucket_nuc(0);
#pragma omp for schedule(dynamic, number_bucket_per_mphf.value())
for (uint64_t BC = (begin_BC); BC < end_BC; ++BC) {
if (nuc_minimizer[BC] != 0) {
largest_bucket_nuc = max(largest_bucket_nuc, nuc_minimizer[BC]);
largest_bucket_nuc_all = max(largest_bucket_nuc_all, nuc_minimizer[BC]);
uint32_t bucketSize(1);
kmer seq(get_kmer(BC, 0)), rcSeq(rcb(seq)), canon(min_k(seq, rcSeq));
anchors.push_back(canon);
for (uint64_t j(0); (j + k) < nuc_minimizer[BC]; j++) {
if (position_super_kmers[all_mphf[BC].mphf_size + bucketSize]) {
j += k - 1;
if ((j + k) < nuc_minimizer[BC]) {
seq = (get_kmer(BC, j + 1)), rcSeq = (rcb(seq)), canon = (min_k(seq, rcSeq));
anchors.push_back(canon);
bucketSize++;
}
} else {
seq = update_kmer(j + k, BC, seq);
rcSeq = (rcb(seq));
canon = (min_k(seq, rcSeq));
anchors.push_back(canon);
bucketSize++;
}
}
largest_bucket_anchor = max(largest_bucket_anchor, bucketSize);
}
if ((BC + 1) % number_bucket_per_mphf == 0 and not anchors.empty()) {
largest_MPHF = max(largest_MPHF, anchors.size());
all_mphf[BC / number_bucket_per_mphf].kmer_MPHF = new boomphf::mphf<kmer, hasher_t>(anchors.size(), anchors, gammaFactor);
anchors.clear();
largest_bucket_anchor = 0;
largest_bucket_nuc = (0);
}
}
}
}
void kmer_Set_Light::create_mphf_disk(uint64_t begin_BC, uint64_t end_BC, bm::bvector<>& position_super_kmers_local) {
#pragma omp parallel num_threads(coreNumber)
{
uint32_t largest_bucket_anchor(0);
uint32_t largest_bucket_nuc(0);
#pragma omp for schedule(dynamic, number_bucket_per_mphf.value())
for (uint64_t BC = (begin_BC); BC < end_BC; ++BC) {
uint64_t mphfSize(0);
string name(working_dir + "_blkmers" + to_string(BC));
if (nuc_minimizer[BC] != 0) {
ofstream out(name, ofstream::binary | ofstream::trunc);
largest_bucket_nuc = max(largest_bucket_nuc, nuc_minimizer[BC]);
largest_bucket_nuc_all = max(largest_bucket_nuc_all, nuc_minimizer[BC]);
uint32_t bucketSize(1);
kmer seq(get_kmer(BC, 0)), rcSeq(rcb(seq)), canon(min_k(seq, rcSeq));
out.write(reinterpret_cast<char*>(&canon), sizeof(canon));
mphfSize++;
for (uint64_t j(0); (j + k) < nuc_minimizer[BC]; j++) {
if (position_super_kmers_local[all_mphf[BC].mphf_size + bucketSize]) {
j += k - 1;
if ((j + k) < nuc_minimizer[BC]) {
seq = (get_kmer(BC, j + 1)), rcSeq = (rcb(seq)), canon = (min_k(seq, rcSeq));
out.write(reinterpret_cast<char*>(&canon), sizeof(canon));
bucketSize++;
mphfSize++;
}
} else {
seq = update_kmer(j + k, BC, seq);
rcSeq = (rcb(seq));
canon = (min_k(seq, rcSeq));
out.write(reinterpret_cast<char*>(&canon), sizeof(canon));
bucketSize++;
mphfSize++;
}
}
largest_bucket_anchor = max(largest_bucket_anchor, bucketSize);
}
if ((BC + 1) % number_bucket_per_mphf == 0 and mphfSize != 0) {
largest_MPHF = max(largest_MPHF, mphfSize);
auto data_iterator = file_binary(name.c_str());
all_mphf[BC / number_bucket_per_mphf].kmer_MPHF = new boomphf::mphf<kmer, hasher_t>(mphfSize, data_iterator, gammaFactor);
remove(name.c_str());
largest_bucket_anchor = 0;
largest_bucket_nuc = (0);
mphfSize = 0;
}
}
}
}
void kmer_Set_Light::int_to_bool(uint64_t n_bits_to_encode, uint64_t X, uint64_t pos, uint64_t start) {
uint64_t i_mutex(((pos * n_bits_to_encode + start) / 1024) * 4096 / (positions_int));
positions_mutex[i_mutex].lock();
for (uint64_t i(0); i < n_bits_to_encode; ++i) {
uint64_t pos_check(i + pos * n_bits_to_encode + start);
if ((pos_check / 1024) * 4096 / (positions_int) != i_mutex) {
positions_mutex[i_mutex].unlock();
i_mutex++;
positions_mutex[i_mutex].lock();
}
positions[pos_check] = X % 2;
X >>= 1;
}
positions_mutex[i_mutex].unlock();
}
uint64_t kmer_Set_Light::bool_to_int(uint64_t n_bits_to_encode, uint64_t pos, uint64_t start) {
uint64_t res(0);
uint64_t acc(1);
for (uint64_t i(0); i < n_bits_to_encode; ++i, acc <<= 1) {
if (positions[i + pos * n_bits_to_encode + start]) {
res |= acc;
}
}
return res;
}
void kmer_Set_Light::fill_positions(uint64_t begin_BC, uint64_t end_BC, bm::bvector<>& position_super_kmers_local) {
#pragma omp parallel for num_threads(coreNumber)
for (uint64_t BC = (begin_BC); BC < end_BC; ++BC) {
uint64_t super_kmer_id(0);
if (nuc_minimizer[BC] > 0) {
uint64_t kmer_id(1);
int n_bits_to_encode(all_mphf[BC / number_bucket_per_mphf].bit_to_encode);
kmer seq(get_kmer(BC, 0)), rcSeq(rcb(seq)), canon(min_k(seq, rcSeq));
int_to_bool(n_bits_to_encode,super_kmer_id / positions_to_check.value(),all_mphf[BC / number_bucket_per_mphf].kmer_MPHF->lookup(canon),all_mphf[BC / number_bucket_per_mphf].start);
for (uint64_t j(0); (j + k) < nuc_minimizer[BC]; j++) {
if (position_super_kmers_local[all_mphf[BC].mphf_size + kmer_id]) {
j += k - 1;
super_kmer_id++;
kmer_id++;
if ((j + k) < nuc_minimizer[BC]) {
seq = (get_kmer(BC, j + 1)), rcSeq = (rcb(seq)), canon = (min_k(seq, rcSeq));
int_to_bool(n_bits_to_encode,super_kmer_id / positions_to_check.value(),all_mphf[BC / number_bucket_per_mphf].kmer_MPHF->lookup(canon), all_mphf[BC / number_bucket_per_mphf].start);
}
} else {
seq = update_kmer(j + k, BC, seq);
rcSeq = (rcb(seq));
canon = (min_k(seq, rcSeq));
kmer_id++;
int_to_bool(n_bits_to_encode,super_kmer_id / positions_to_check.value(),all_mphf[BC / number_bucket_per_mphf].kmer_MPHF->lookup(canon), all_mphf[BC / number_bucket_per_mphf].start);
}
}
}
}
}
int64_t kmer_Set_Light::kmer_to_hash(const kmer canon, kmer minimizer) {
if (unlikely(all_mphf[minimizer / number_bucket_per_mphf].empty)) {
return -1;
}
uint64_t hash = (all_mphf[minimizer / number_bucket_per_mphf].kmer_MPHF->lookup(canon));
uint64_t pos;
if (unlikely(hash == ULLONG_MAX)) {
return -1;
} else {
return hash;
}
}
int64_t kmer_Set_Light::hash_to_rank(const int64_t hash, kmer minimizer) {
int n_bits_to_encode(all_mphf[minimizer / number_bucket_per_mphf].bit_to_encode);
int64_t rank(all_buckets[minimizer].skmer_number + bool_to_int(n_bits_to_encode, hash, all_mphf[minimizer / number_bucket_per_mphf].start) * positions_to_check.value());
return rank;
}
vector<kmer> kmer_Set_Light::kmer_to_superkmer(const kmer canon, kmer minimizer, int64_t& rank, int64_t& hash) {
hash = kmer_to_hash(canon, minimizer);
if (hash < 0) {
return {};
}
rank = (hash_to_rank(hash, minimizer));
if (rank < 0) {
return {};
}
vector<kmer> result;
bool found(false);
bm::id64_t pos, next_position, stop_position;
position_super_kmers.select(rank + 1, pos, *(position_super_kmers_RS));
for (uint64_t check_super_kmer(0); check_super_kmer < positions_to_check.value() and not found; ++check_super_kmer) {
next_position = (position_super_kmers.get_next(pos));
if (next_position == 0) {
stop_position = bucketSeq.size() - k;
} else {
stop_position = next_position + (rank + check_super_kmer) * (k - 1);
}
pos += (rank + check_super_kmer) * (k - 1);
if (likely(((uint64_t)pos + k - 1) < bucketSeq.size())) {
kmer seqR = get_kmer(pos);
kmer rcSeqR, canonR;
for (uint64_t j = (pos); j < stop_position; ++j) {
rcSeqR = (rcb(seqR));
canonR = (min_k(seqR, rcSeqR));
result.push_back(canonR);
if (canon == canonR) {
found = true;
}
if (likely(((j + k) * 2 < bucketSeq.size()))) {
seqR = update_kmer_local(j + k, bucketSeq, seqR);
}
}
}
pos = next_position;
}
if (found) {
return result;
}
return {};
}
vector<bool> kmer_Set_Light::get_presence_query(const string& query) {
if (query.size() < k) {
return {};
}
vector<bool> result;
kmer seq(str2num(query.substr(0, k))), rcSeq(rcb(seq)), canon(min_k(seq, rcSeq));
int64_t i(0), rank, hash;
vector<kmer> superKmers;
kmer minimizer(regular_minimizer(canon));
for (; i + k <= query.size(); ++i) {
if (superKmers.empty()) {
superKmers = kmer_to_superkmer(canon, minimizer, rank, hash);
result.push_back(not superKmers.empty());
} else {
if (kmer_in_superkmer(canon, superKmers)) {
result.push_back(true);
} else {
superKmers = kmer_to_superkmer(canon, minimizer, rank, hash);
result.push_back(not superKmers.empty());
}
}
if (i + k < query.size()) {
updateK(seq, query[i + k]);
updateRCK(rcSeq, query[i + k]);
canon = (min_k(seq, rcSeq));
minimizer = (regular_minimizer(canon));
}
}
return result;
}
vector<int64_t> kmer_Set_Light::get_rank_query(const string& query) {
if (query.size() < k) {
return {};
}
vector<int64_t> result;
kmer seq(str2num(query.substr(0, k))), rcSeq(rcb(seq)), canon(min_k(seq, rcSeq));
int64_t i(0), rank, hash;
vector<kmer> superKmers;
kmer minimizer(regular_minimizer(canon));
for (; i + k <= query.size(); ++i) {
if (superKmers.empty()) {
superKmers = kmer_to_superkmer(canon, minimizer, rank, hash);
result.push_back(superKmers.empty() ? -1 : rank);
} else {