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Amrfinder threads bugfix #290

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Merged
andrewdavidsmith merged 1 commit into from
Aug 28, 2025
Merged

Amrfinder threads bugfix #290

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60 changes: 29 additions & 31 deletions src/amrfinder/amrfinder.cpp
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Original file line number Diff line number Diff line change
@@ -1,20 +1,20 @@
/* amrfinder: program for resolving epialleles in a sliding window
* along a chromosome.
/* amrfinder: program for resolving epialleles in a sliding window along a
* chromosome.
*
* Copyright (C) 2014-2025 University of Southern California and
* Copyright (C) 2014-2025 University of Southern California
* Andrew D. Smith and Benjamin E. Decato
*
* Authors: Fang Fang and Benjamin E. Decato and Andrew D. Smith
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
* This program is free software: you can redistribute it and/or modify it
* under the terms of the GNU General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option)
* any later version.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* General Public License for more details.
* This program is distributed in the hope that it will be useful, but WITHOUT
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
* more details.
*/

#include "EpireadStats.hpp"
Expand All @@ -34,8 +34,6 @@
#include <thread>
#include <vector>

using bamxx::bgzf_file;

struct amr_summary {
amr_summary(const std::vector<GenomicRegion> &amrs) {
amr_count = std::size(amrs);
Expand Down Expand Up @@ -80,7 +78,7 @@ read_epiread(bamxx::bgzf_file &f, epiread &er) {
static inline bool
validate_epiread_bgzf_file(const std::string &filename) {
constexpr std::size_t max_lines_to_validate = 10000;
bgzf_file in(filename, "r");
bamxx::bgzf_file in(filename, "r");
if (!in)
throw std::runtime_error("failed to open file: " + filename);

Expand Down Expand Up @@ -219,14 +217,14 @@ convert_coordinates(const std::size_t n_threads, const std::string &genome_file,
std::atomic_uint32_t conv_failure = 0;

std::vector<std::thread> threads;
for (auto i = 0ul; i < n_threads; ++i) {
const auto p_beg = parts_beg + i * n_per;
for (auto i = 0ul; i < std::min(n_threads, n_parts); ++i) {
const auto p_beg = parts_beg + std::min(i * n_per, n_parts);
const auto p_end = parts_beg + std::min((i + 1) * n_per, n_parts);
threads.emplace_back([&, p_beg, p_end] {
for (auto p = p_beg; p != p_end; ++p) {
const std::string chrom_name = amrs[p->first].get_chrom();
auto c_itr = chrom_lookup.find(chrom_name);
if (c_itr == std::end(chrom_lookup))
const auto c_itr = chrom_lookup.find(chrom_name);
if (c_itr == std::cend(chrom_lookup))
conv_failure++;
else {
std::vector<std::uint32_t> cpgs = collect_cpgs(c_itr->second);
Expand Down Expand Up @@ -335,7 +333,7 @@ process_chrom(const bool verbose, const std::uint32_t n_threads,
if (verbose)
std::cerr << "processing " << chrom_name << " "
<< "[reads: " << std::size(epireads) << "] "
<< "[cpgs: " << n_cpgs << "]" << std::endl;
<< "[cpgs: " << n_cpgs << "]\n";

const auto n_blocks = n_threads * blocks_per_thread;

Expand Down Expand Up @@ -462,20 +460,20 @@ main_amrfinder(int argc, char *argv[]) {
std::vector<std::string> leftover_args;
opt_parse.parse(argc, argv, leftover_args);
if (argc == 1 || opt_parse.help_requested()) {
std::cerr << opt_parse.help_message() << std::endl
<< opt_parse.about_message() << std::endl;
std::cerr << opt_parse.help_message() << '\n'
<< opt_parse.about_message() << '\n';
return EXIT_SUCCESS;
}
if (opt_parse.about_requested()) {
std::cerr << opt_parse.about_message() << std::endl;
std::cerr << opt_parse.about_message() << '\n';
return EXIT_SUCCESS;
}
if (opt_parse.option_missing()) {
std::cerr << opt_parse.option_missing_message() << std::endl;
std::cerr << opt_parse.option_missing_message() << '\n';
return EXIT_SUCCESS;
}
if (leftover_args.size() != 1) {
std::cerr << opt_parse.help_message() << std::endl;
if (std::size(leftover_args) != 1) {
std::cerr << opt_parse.help_message() << '\n';
return EXIT_SUCCESS;
}
const std::string reads_file(leftover_args.front());
Expand All @@ -489,13 +487,13 @@ main_amrfinder(int argc, char *argv[]) {
if (verbose)
std::cerr << "AMR TESTING OPTIONS: "
<< "[test=" << (use_bic ? "BIC" : "LRT") << "] "
<< "[iterations=" << max_itr << "]" << std::endl;
<< "[iterations=" << max_itr << "]\n";

const EpireadStats epistat{low_prob, high_prob, critical_value,
max_itr, use_bic, correct_for_read_count};

bamxx::bam_tpool tp(n_threads);
bgzf_file in(reads_file, "r");
bamxx::bgzf_file in(reads_file, "r");
if (!in)
throw std::runtime_error("failed to open input file: " + reads_file);
if (n_threads > 1 && in.is_bgzf())
Expand Down Expand Up @@ -533,7 +531,7 @@ main_amrfinder(int argc, char *argv[]) {
std::for_each(std::begin(amrs), std::end(amrs), rename_amr());

if (verbose)
std::cerr << "========= POST PROCESSING =========" << std::endl;
std::cerr << "========= POST PROCESSING =========\n";

// windows_accepted is the number of sliding windows in the
// methylome that were found to have a significant signal of
Expand Down Expand Up @@ -592,7 +590,7 @@ main_amrfinder(int argc, char *argv[]) {
const auto n_collapsed_amrs = std::size(amrs);

if (!convert_coordinates(n_threads, genome_file, amrs)) {
std::cerr << "failed converting coordinates" << std::endl;
std::cerr << "failed converting coordinates\n";
return EXIT_FAILURE;
}

Expand Down Expand Up @@ -650,11 +648,11 @@ main_amrfinder(int argc, char *argv[]) {
std::ofstream summary_out(summary_file);
if (!summary_out)
throw std::runtime_error("failed to open: " + summary_file);
summary_out << amr_summary(amrs).tostring() << std::endl;
summary_out << amr_summary(amrs).tostring() << '\n';
}
}
catch (const std::exception &e) {
std::cerr << e.what() << std::endl;
std::cerr << e.what() << '\n';
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
Expand Down