Étienne Mollier pushed to branch upstream at Debian Med / quorum
Commits: 71bb14ab by Étienne Mollier at 2023-06-14T22:15:24+02:00 New upstream version 1.1.2 - - - - - 4 changed files: - configure.ac - src/create_database.cc - src/err_log.hpp - src/error_correct_reads.cc Changes: ===================================== configure.ac ===================================== @@ -1,4 +1,4 @@ -AC_INIT([quorum], [1.1.1], [[email protected]]) +AC_INIT([quorum], [1.1.2], [[email protected]]) AC_CONFIG_AUX_DIR([build-aux]) AC_CONFIG_SRCDIR([src/error_correct_reads.hpp]) AC_CONFIG_HEADERS([config.h]) @@ -55,6 +55,21 @@ AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x]) AC_CHECK_TYPE([__int128], [AC_DEFINE([HAVE_INT128], [1], [Define if type __int128 is supported])]) +# Check that type __int128 is supported and if the +# std::numeric_limits<__int128> specialization exists +AC_ARG_WITH([int128], + [AS_HELP_STRING([--with-int128], [enable int128])], + [], [with_int128=yes]) +AS_IF([test "x$with_int128" != xno], + [AC_CHECK_TYPE([__int128], + [AC_DEFINE([HAVE_INT128], [1], [Define if type __int128 is supported])]) + AC_MSG_CHECKING([for std::numeric_limits<__int128>]) + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <limits> + template<bool> struct StaticAssert; template<> struct StaticAssert<true> { static void assert() { } };]], + [[StaticAssert<std::numeric_limits<__int128>::is_specialized>::assert();]])], + [AC_MSG_RESULT([yes])] + [AC_DEFINE([HAVE_NUMERIC_LIMITS128], [1], [Define if numeric limits specialization exists for __int128])], + [AC_MSG_RESULT([no])])]) # Check the version of strerror_r ===================================== src/create_database.cc ===================================== @@ -55,7 +55,6 @@ public: virtual void start(int thid) { mer_dna m, rm; - size_t counted_high = 0, counted_low = 0; while(true) { read_parser::job job(parser_); @@ -85,8 +84,6 @@ public: if(low_len >= mer_dna::k()) { if(!ary_.add(m < rm ? m : rm, high_len >= mer_dna::k())) throw std::runtime_error(err::msg() << "Hash is full"); - counted_high += high_len >= mer_dna::k(); - ++counted_low; } } } ===================================== src/err_log.hpp ===================================== @@ -39,7 +39,7 @@ private: entry(type_t t, T p) : type(t), pos(p) {} }; - struct greater_than_pos : std::unary_function<entry, bool> { + struct greater_than_pos { T pos; bool operator()(entry& e) { return e.pos >= *pos; } // Compare the raw value of pos, not using the operator>= greater_than_pos(T& pos_) : pos(pos_) { } ===================================== src/error_correct_reads.cc ===================================== @@ -161,9 +161,9 @@ public: std::unique_ptr<std::ostream> output(open_file(_prefix, ".fa", "/dev/fd/1")); // Multiplexers, same thing std::unique_ptr<jflib::o_multiplexer> - log_m(new jflib::o_multiplexer(details.get(), 3 * nb_threads, 1024)); + log_m(new jflib::o_multiplexer(details.get(), 3 * (size_t)nb_threads, 1024)); std::unique_ptr<jflib::o_multiplexer> - output_m(new jflib::o_multiplexer(output.get(), 3 * nb_threads, 1024)); + output_m(new jflib::o_multiplexer(output.get(), 3 * (size_t)nb_threads, 1024)); _log = log_m.get(); _output = output_m.get(); @@ -248,7 +248,6 @@ public: jflib::omstream details(_ec.log()); kmer_t mer, tmer; - uint64_t nb_reads = 0; while(true) { read_parser::job job(_ec.parser()); if(job.is_empty()) break; @@ -261,7 +260,6 @@ public: const char* const seq_e = seq_s + sequence.size(); const char* const qual_s = job->data[i].qual.c_str(); - nb_reads++; insure_length_buffer(sequence.size()); const char* error = ""; View it on GitLab: https://salsa.debian.org/med-team/quorum/-/commit/71bb14abbc544797133f2e9ff66624f2afb88349 -- View it on GitLab: https://salsa.debian.org/med-team/quorum/-/commit/71bb14abbc544797133f2e9ff66624f2afb88349 You're receiving this email because of your account on salsa.debian.org.
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