Radmeth optimizations for continuous values

Makefile.am

@@ -189,8 +189,12 @@ libdnmtools_a_SOURCES += \
 # ADS: additional radmeth sources to help isolate the parts using GSL for
 # optimization
 libdnmtools_a_SOURCES += \
-        src/radmeth/radmeth_optimize.hpp \
-        src/radmeth/radmeth_model.hpp
+        src/radmeth/radmeth_optimize_series.hpp \
+        src/radmeth/radmeth_optimize_gamma.hpp \
+        src/radmeth/radmeth_optimize_params.hpp \
+        src/radmeth/radmeth_model.hpp \
+        src/radmeth/radmeth_utils.hpp \
+        src/radmeth/radmeth_design.hpp
 
 LDADD = libdnmtools.a src/abismal/libabismal.a src/smithlab_cpp/libsmithlab_cpp.a
 
@@ -236,9 +240,12 @@ dnmtools_SOURCES += src/amrfinder/amrtester.cpp
 
 dnmtools_SOURCES += src/radmeth/dmr.cpp
 dnmtools_SOURCES += src/radmeth/methdiff.cpp
-dnmtools_SOURCES += src/radmeth/radmeth_optimize.cpp
-dnmtools_SOURCES += src/radmeth/radmeth_model.cpp
+dnmtools_SOURCES += src/radmeth/radmeth_utils.cpp
+dnmtools_SOURCES += src/radmeth/radmeth_optimize_series.cpp
+dnmtools_SOURCES += src/radmeth/radmeth_optimize_gamma.cpp
+dnmtools_SOURCES += src/radmeth/radmeth_design.cpp
 dnmtools_SOURCES += src/radmeth/radmeth.cpp
+dnmtools_SOURCES += src/radmeth/radmeth_nano.cpp
 dnmtools_SOURCES += src/radmeth/radmeth-adjust.cpp
 dnmtools_SOURCES += src/radmeth/radmeth-merge.cpp
 

src/analysis/nanopore.cpp

@@ -845,7 +845,8 @@ struct read_processor {
     if (chrom_name == nullptr)
       throw std::runtime_error("failed to identify chrom for tid: " +
                                std::to_string(tid));
-    const auto chrom_name_offset = std::sprintf(buffer, "%s\t", chrom_name);
+    const auto chrom_name_offset =
+      std::snprintf(buffer, buf_size, "%s\t", chrom_name);
     if (chrom_name_offset < 0)
       throw std::runtime_error("failed to write to output buffer");
     auto buffer_after_chrom = buffer + chrom_name_offset;
@@ -869,14 +870,16 @@ struct read_processor {
         const double mods = counts[chrom_posn].get_mods(is_c) / denom;
 
         // clang-format off
-        const int r = std::sprintf(buffer_after_chrom, out_fmt,
-                                   chrom_posn,
-                                   is_c ? '+' : '-',
-                                   tag_values[the_tag],
-                                   mods,
-                                   n_reads,
-                                   hydroxy,
-                                   methyl);
+        const int r = std::snprintf(buffer_after_chrom,
+                                    buf_size - chrom_name_offset,
+                                    out_fmt,
+                                    chrom_posn,
+                                    is_c ? '+' : '-',
+                                    tag_values[the_tag],
+                                    mods,
+                                    n_reads,
+                                    hydroxy,
+                                    methyl);
         // clang-format on
 
         if (r < 0)
@@ -900,7 +903,8 @@ struct read_processor {
     if (chrom_name == nullptr)
       throw std::runtime_error("failed to identify chrom for tid: " +
                                std::to_string(tid));
-    const auto chrom_name_offset = std::sprintf(buffer, "%s\t", chrom_name);
+    const auto chrom_name_offset =
+      std::snprintf(buffer, buf_size, "%s\t", chrom_name);
     if (chrom_name_offset < 0)
       throw std::runtime_error("failed to write to output buffer");
     auto buffer_after_chrom = buffer + chrom_name_offset;
@@ -935,12 +939,14 @@ struct read_processor {
           const auto mods = hydroxy + methyl;
 
           // clang-format off
-          const int r = std::sprintf(buffer_after_chrom, out_fmt,
-                                     chrom_posn - 1,  // for previous position
-                                     mods,
-                                     n_reads,
-                                     hydroxy,
-                                     methyl);
+          const int r = std::snprintf(buffer_after_chrom,
+                                      buf_size - chrom_name_offset,
+                                      out_fmt,
+                                      chrom_posn - 1,  // for previous position
+                                      mods,
+                                      n_reads,
+                                      hydroxy,
+                                      methyl);
           // clang-format on
 
           if (r < 0)

src/dnmtools.cpp

@@ -111,6 +111,8 @@ main_radmeth_adjust(int argc, char *argv[]);
 int
 main_radmeth(int argc, char *argv[]);
 int
+main_radmeth_nano(int argc, char *argv[]);
+int
 main_radmeth_merge(int argc, char *argv[]);
 int
 main_clean_hairpins(int argc, char *argv[]);
@@ -204,6 +206,7 @@ main(int argc, char *argv[]) {
  {{{"dmr",       "identify DMRs from genomic intervals and single-CpG DM probabilities",  main_dmr},
    {"diff",      "compute single-CpG DM probability between two methylomes", main_methdiff},
    {"radmeth",   "compute DM probabilities for each CpG using multiple methylomes", main_radmeth},
+   {"radmeth-nano", "radmeth designed for nanopore data", main_radmeth_nano},
    {"radadjust", "adjust p-values from radmeth output", main_radmeth_adjust},
    {"radmerge",  "merge significant CpGs in radmeth output", main_radmeth_merge}}}},
 

src/radmeth/methdiff.cpp

@@ -105,16 +105,16 @@ write_methdiff_site(T &out, const MSite &a, const MSite &b,
   static char buffer[buf_size];
 
   // clang-format off
-  const int r = std::sprintf(buffer, out_fmt,
-                             a.chrom.data(),
-                             a.pos,
-                             a.strand,
-                             a.context.data(),
-                             diffscore,
-                             a.n_meth(),
-                             a.n_unmeth(),
-                             b.n_meth(),
-                             b.n_unmeth());
+  const int r = std::snprintf(buffer, buf_size, out_fmt,
+                              a.chrom.data(),
+                              a.pos,
+                              a.strand,
+                              a.context.data(),
+                              diffscore,
+                              a.n_meth(),
+                              a.n_unmeth(),
+                              b.n_meth(),
+                              b.n_unmeth());
   // clang-format on
   if (r < 0)
     throw std::runtime_error("failed to write to output buffer");