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xcounts: improved how chromosome order inconsistencies are detected #301

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Merged
andrewdavidsmith merged 1 commit into from
Oct 14, 2025
Merged

xcounts: improved how chromosome order inconsistencies are detected #301

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27 changes: 19 additions & 8 deletions src/utils/xcounts.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
#include <string>
#include <system_error>
#include <type_traits> // std::underlying_type_t
#include <unordered_set>
#include <vector>

enum class xcounts_err {
Expand Down Expand Up @@ -69,7 +70,7 @@ struct xcounts_err_cat : std::error_category {
std::abort(); // unreacheable
}
};
// clang-format off
// clang-format on

template <>
struct std::is_error_code_enum<xcounts_err> : public std::true_type {};
Expand Down Expand Up @@ -97,6 +98,9 @@ fill_output_buffer(const std::uint32_t offset, const MSite &s, T &buf) {
int
main_xcounts(int argc, char *argv[]) {
try {
// ADS: It might happen that a "chromosome" has no CpG sites (like
// Scaffold113377 in strPur2). Therefore, we can't assume each chrom will
// appear in the input when attempting to check consistency.
bool verbose = false;
bool gzip_output = false;
bool keep_all_sites = false;
Expand All @@ -116,7 +120,8 @@ main_xcounts(int argc, char *argv[]) {
false, outfile);
opt_parse.add_opt("chroms", 'c', "make header from this reference", false,
genome_file);
opt_parse.add_opt("reads", 'r', "output only sites with reads (on by default)", false,
opt_parse.add_opt("reads", 'r',
"output only sites with reads (on by default)", false,
require_coverage);
opt_parse.add_opt("keep", 'k', "keep sites that are not covered", false,
keep_all_sites);
Expand Down Expand Up @@ -177,6 +182,7 @@ main_xcounts(int argc, char *argv[]) {
}

std::unordered_map<std::string, std::uint32_t> chrom_order;
std::unordered_set<std::uint32_t> chroms_seen;
if (!header_file.empty())
chrom_order = write_counts_header_from_file(header_file, out);
else if (!genome_file.empty())
Expand Down Expand Up @@ -224,15 +230,20 @@ main_xcounts(int argc, char *argv[]) {
std::cerr << "processing: " << site.chrom << '\n';

if (!chrom_order.empty()) {
const auto expected_chrom_counter = chrom_order.find(site.chrom);
if (expected_chrom_counter == std::cend(chrom_order)) {
const auto expected_chrom_order = chrom_order.find(site.chrom);
if (expected_chrom_order == std::cend(chrom_order)) {
ec = xcounts_err::chromosome_not_found;
break;
}
if (expected_chrom_counter->second != chrom_counter) {
if (expected_chrom_order->second < chrom_counter) {
ec = xcounts_err::inconsistent_chromosome_order;
break;
}
if (chroms_seen.count(expected_chrom_order->second) > 0) {
ec = xcounts_err::inconsistent_chromosome_order;
break;
}
chroms_seen.emplace(expected_chrom_order->second);
}

++chrom_counter;
Expand All @@ -241,12 +252,12 @@ main_xcounts(int argc, char *argv[]) {
offset = 0;

site.chrom += '\n';
const int64_t sz = size(site.chrom);
const std::int64_t sz = size(site.chrom);
if (bgzf_write(out.f, site.chrom.data(), sz) != sz)
ec = xcounts_err::failed_to_write_file;
}
if (keep_all_sites || site.n_reads > 0) {
const int64_t sz = fill_output_buffer(offset, site, buf);
const std::int64_t sz = fill_output_buffer(offset, site, buf);
if (bgzf_write(out.f, buf.data(), sz) != sz)
ec = xcounts_err::failed_to_write_file;
offset = site.pos;
Expand All @@ -256,7 +267,7 @@ main_xcounts(int argc, char *argv[]) {

if (ec) {
std::cerr << "failed converting " << filename << " to " << outfile << '\n'
<< ec.message() << '\n';
<< ec.message() << '\n';
return EXIT_FAILURE;
}
}
Expand Down
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