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andrewdavidsmith merged 1 commit into from
Aug 28, 2025
Merged

Better error reporting for xcounts #289

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114 changes: 52 additions & 62 deletions src/utils/xcounts.cpp
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Original file line number Diff line number Diff line change
@@ -1,51 +1,41 @@
/* xcounts: reformat counts so they only give the m and u counts in a
* dynamic step wig format
/* xcounts: reformat counts so they only give the m and u counts in a dynamic
* step wig format
*
* Copyright (C) 2023 Andrew D. Smith
*
* Authors: 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 "MSite.hpp"
#include "counts_header.hpp"
#include "dnmt_error.hpp"

#include <bamxx.hpp>

// from smithlab_cpp
#include "OptionParser.hpp"
#include "smithlab_os.hpp"
#include "smithlab_utils.hpp"

#include <charconv>
#include <cstdint>
#include <iostream>
#include <stdexcept>
#include <string>
#include <system_error>
#include <type_traits> // std::underlying_type_t
#include <vector>

// from smithlab_cpp
#include "OptionParser.hpp"
#include "smithlab_os.hpp"
#include "smithlab_utils.hpp"

#include "MSite.hpp"
#include "counts_header.hpp"
#include "dnmt_error.hpp"

using std::cerr;
using std::cout;
using std::endl;
using std::runtime_error;
using std::string;
using std::to_chars;
using std::to_string;
using std::vector;

using bamxx::bgzf_file;

enum class xcounts_err {
// clang-format off
ok = 0,
Expand Down Expand Up @@ -92,14 +82,14 @@ make_error_code(xcounts_err e) {
}

template <typename T>
static inline uint32_t
fill_output_buffer(const uint32_t offset, const MSite &s, T &buf) {
static inline std::uint32_t
fill_output_buffer(const std::uint32_t offset, const MSite &s, T &buf) {
auto buf_end = buf.data() + buf.size();
auto res = to_chars(buf.data(), buf_end, s.pos - offset);
auto res = std::to_chars(buf.data(), buf_end, s.pos - offset);
*res.ptr++ = '\t';
res = to_chars(res.ptr, buf_end, s.n_meth());
res = std::to_chars(res.ptr, buf_end, s.n_meth());
*res.ptr++ = '\t';
res = to_chars(res.ptr, buf_end, s.n_unmeth());
res = std::to_chars(res.ptr, buf_end, s.n_unmeth());
*res.ptr++ = '\n';
return std::distance(buf.data(), res.ptr);
}
Expand All @@ -111,12 +101,12 @@ main_xcounts(int argc, char *argv[]) {
bool gzip_output = false;
bool keep_all_sites = false;
bool require_coverage = false;
size_t n_threads = 1;
string genome_file;
string header_file;
std::size_t n_threads = 1;
std::string genome_file;
std::string header_file;

string outfile{"-"};
const string description =
std::string outfile{"-"};
const std::string description =
"compress counts files by removing context information";

/****************** COMMAND LINE OPTIONS ********************/
Expand All @@ -138,30 +128,30 @@ main_xcounts(int argc, char *argv[]) {
"gzip compress output (automatic if input is gzip)",
false, gzip_output);
opt_parse.add_opt("verbose", 'v', "print more run info", false, verbose);
std::vector<string> leftover_args;
std::vector<std::string> leftover_args;
opt_parse.parse(argc, argv, leftover_args);
if (argc == 1 || opt_parse.help_requested()) {
cerr << opt_parse.help_message() << endl
<< opt_parse.about_message() << endl;
std::cerr << opt_parse.help_message() << '\n'
<< opt_parse.about_message() << '\n';
return EXIT_SUCCESS;
}
if (opt_parse.about_requested()) {
cerr << opt_parse.about_message() << endl;
std::cerr << opt_parse.about_message() << '\n';
return EXIT_SUCCESS;
}
if (opt_parse.option_missing()) {
cerr << opt_parse.option_missing_message() << endl;
std::cerr << opt_parse.option_missing_message() << '\n';
return EXIT_SUCCESS;
}
if (leftover_args.size() != 1) {
cerr << opt_parse.help_message() << endl;
std::cerr << opt_parse.help_message() << '\n';
return EXIT_SUCCESS;
}
const string filename(leftover_args.front());
const std::string filename(leftover_args.front());
/****************** END COMMAND LINE OPTIONS *****************/

vector<string> chrom_names;
vector<uint64_t> chrom_sizes;
std::vector<std::string> chrom_names;
std::vector<std::uint64_t> chrom_sizes;
if (!genome_file.empty()) {
const int ret = get_chrom_sizes_for_counts_header(
n_threads, genome_file, chrom_names, chrom_sizes);
Expand All @@ -170,13 +160,13 @@ main_xcounts(int argc, char *argv[]) {
}

bamxx::bam_tpool tpool(n_threads);
bgzf_file in(filename, "r");
bamxx::bgzf_file in(filename, "r");
if (!in)
throw dnmt_error{"could not open file: " + filename};

const auto outfile_mode = (gzip_output || in.is_compressed()) ? "w" : "wu";

bgzf_file out(outfile, outfile_mode);
bamxx::bgzf_file out(outfile, outfile_mode);
if (!out)
throw dnmt_error{"error opening output file: " + outfile};

Expand All @@ -186,7 +176,7 @@ main_xcounts(int argc, char *argv[]) {
tpool.set_io(out);
}

std::unordered_map<string, uint32_t> chrom_order;
std::unordered_map<std::string, std::uint32_t> chrom_order;
if (!header_file.empty())
chrom_order = write_counts_header_from_file(header_file, out);
else if (!genome_file.empty())
Expand All @@ -199,23 +189,23 @@ main_xcounts(int argc, char *argv[]) {
if (ret)
throw dnmt_error("failed to acquire buffer");

vector<char> buf(128);
std::vector<char> buf(128);

uint32_t offset = 0;
string prev_chrom;
std::uint32_t offset = 0;
std::string prev_chrom;
bool found_header = (!genome_file.empty() || !header_file.empty());

std::error_code ec{};

uint32_t chrom_counter = 0;
std::uint32_t chrom_counter = 0;

MSite site;
while (ec == std::errc{} && bamxx::getline(in, line)) {
if (is_counts_header_line(line.s)) {
if (!genome_file.empty() || !header_file.empty())
continue;
found_header = true;
const string header_line{line.s};
const std::string header_line{line.s};
write_counts_header_line(header_line, out);
continue;
}
Expand All @@ -231,7 +221,7 @@ main_xcounts(int argc, char *argv[]) {

if (site.chrom != prev_chrom) {
if (verbose)
cerr << "processing: " << site.chrom << endl;
std::cerr << "processing: " << site.chrom << '\n';

if (!chrom_order.empty()) {
const auto expected_chrom_counter = chrom_order.find(site.chrom);
Expand All @@ -245,7 +235,7 @@ main_xcounts(int argc, char *argv[]) {
}
}

chrom_counter++;
++chrom_counter;

prev_chrom = site.chrom;
offset = 0;
Expand All @@ -265,13 +255,13 @@ main_xcounts(int argc, char *argv[]) {
ks_free(&line);

if (ec) {
cerr << "failed converting " << filename << " to " << outfile << endl
<< ec << endl;
std::cerr << "failed converting " << filename << " to " << outfile << '\n'
<< ec.message() << '\n';
return EXIT_FAILURE;
}
}
catch (const std::exception &e) {
cerr << e.what() << endl;
std::cerr << e.what() << '\n';
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
Expand Down