From cee4bfeb42639c4bd48d47b815c085f0e649c255 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Tue, 29 Sep 2026 11:03:36 -0700 Subject: [PATCH 1/4] src/kmer_counter.cpp and src/falco_file_format.hpp: consistency on function signature specifiers --- src/falco_file_format.hpp | 8 ++++---- src/kmer_counter.cpp | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/falco_file_format.hpp b/src/falco_file_format.hpp index 2bb5253..8d1f606 100644 --- a/src/falco_file_format.hpp +++ b/src/falco_file_format.hpp @@ -52,22 +52,22 @@ NLOHMANN_JSON_SERIALIZE_ENUM( }) // clang-format on -[[nodiscard]] constexpr inline auto +[[nodiscard]] inline constexpr auto is_mapped_reads(const file_format f) { return f == file_format::sam || f == file_format::bam; } -[[nodiscard]] constexpr inline auto +[[nodiscard]] inline constexpr auto is_bam(const file_format f) { return f == file_format::bam; } -[[nodiscard]] constexpr inline auto +[[nodiscard]] inline constexpr auto is_bgzf(const file_format f) { return f == file_format::bam || f == file_format::fastq_bgzf; } -[[nodiscard]] constexpr inline auto +[[nodiscard]] inline constexpr auto is_plain(const file_format f) { return f == file_format::sam || f == file_format::fastq; } diff --git a/src/kmer_counter.cpp b/src/kmer_counter.cpp index e457cd8..e950555 100644 --- a/src/kmer_counter.cpp +++ b/src/kmer_counter.cpp @@ -66,7 +66,7 @@ gamma_p_series(const double a, const double x) -> double { return sum * std::exp(-x + a * std::log(x) - std::lgamma(a)); } -[[nodiscard]] static constexpr inline auto +[[nodiscard]] static inline constexpr auto safe_floor(const auto x, const auto floor_val) { return std::abs(x) < floor_val ? floor_val : x; } From c71dc67af6d4b58e1edf9f2ac1d80e98cfa01e25 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Wed, 30 Sep 2026 12:00:39 -0700 Subject: [PATCH 2/4] src/falco.cpp: fixing misleading help message --- src/falco.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/falco.cpp b/src/falco.cpp index d9356eb..64e8377 100644 --- a/src/falco.cpp +++ b/src/falco.cpp @@ -374,7 +374,8 @@ main(int argc, char *argv[]) { app.add_option("-m,--mem", buffer_size, "Input memory buffer size (G/M/K units ok)") ->check(CLI::Range(min_buf_size, max_buf_size)) - ->option_text(std::format("[{}]", size_to_units(buffer_size_default))) + ->option_text(std::format("[{}]", + size_to_units(buffer_size_default, ""))) ->capture_default_str() ->transform(size_from_units); app.add_flag("-v,--verbose", verbose, "Print more info about the run") From 8a7a955f16ba19370338fbbd5049f7314b901ecd Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Wed, 30 Sep 2026 12:11:23 -0700 Subject: [PATCH 3/4] src/falco.cpp: fixing verbose output of memory buffer size --- src/falco.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/falco.cpp b/src/falco.cpp index 64e8377..9680f51 100644 --- a/src/falco.cpp +++ b/src/falco.cpp @@ -532,7 +532,7 @@ main(int argc, char *argv[]) { "threads requested: {}\n" "input memory buffer size: {}\n" "max analyzable read length: {}\n", - n_threads, size_to_units(buffer_size), + n_threads, size_to_units(buffer_size, "B"), size_to_units(max_read_length, "bp")); std::println("Analyses\n{}", mode.string_verbose()); std::println("Input files"); From e13ee65f60ec1d107e1a7efb7639efff19bc6f4b Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Wed, 30 Sep 2026 12:17:52 -0700 Subject: [PATCH 4/4] src/falco.cpp: formatting --- src/falco.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/falco.cpp b/src/falco.cpp index 9680f51..14fe9b3 100644 --- a/src/falco.cpp +++ b/src/falco.cpp @@ -375,7 +375,7 @@ main(int argc, char *argv[]) { "Input memory buffer size (G/M/K units ok)") ->check(CLI::Range(min_buf_size, max_buf_size)) ->option_text(std::format("[{}]", - size_to_units(buffer_size_default, ""))) + size_to_units(buffer_size_default, ""))) ->capture_default_str() ->transform(size_from_units); app.add_flag("-v,--verbose", verbose, "Print more info about the run")