[med-svn] [Git][med-team/quorum][upstream] New upstream version 1.1.2

[Étienne Mollier (@emollier)]

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], [gmarcais at cs.cmu.edu])
+AC_INIT([quorum], [1.1.2], [gmarcais at cs.cmu.edu])
 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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230614/8dd740a8/attachment-0001.htm>