Merge pull request #205 from smithlabcode/pmd-coverage-and-binsize

pmd guarantee coverage

src/analysis/pmd.cpp

@@ -1064,8 +1064,7 @@ binsize_selection(const size_t resolution, const size_t min_bin_sz,
     if (frac_passed < min_frac_passed)
       bin_size += resolution;
   }
-  return frac_passed <= num_lim<double>::min() ?
-    num_lim<size_t>::max() : bin_size;
+  return frac_passed < min_frac_passed ? num_lim<size_t>::max() : bin_size;
 }
 
 

src/common/counts_header.cpp

@@ -38,9 +38,9 @@ using std::to_string;
 using bamxx::bgzf_file;
 
 void
-write_counts_header_from_chom_sizes(const vector<string> &chrom_names,
-                                    const vector<uint64_t> &chrom_sizes,
-                                    bgzf_file &out) {
+write_counts_header_from_chrom_sizes(const vector<string> &chrom_names,
+                                     const vector<uint64_t> &chrom_sizes,
+                                     bgzf_file &out) {
   const auto version = "#DNMTOOLS " + string(VERSION) + "\n";
   out.write(version.c_str());
   for (auto i = 0u; i < size(chrom_sizes); ++i) {

src/common/counts_header.hpp

@@ -26,9 +26,9 @@
 #include "bamxx.hpp"
 
 void
-write_counts_header_from_chom_sizes(const std::vector<std::string> &chrom_names,
-                                    const std::vector<uint64_t> &chrom_sizes,
-                                    bamxx::bgzf_file &out);
+write_counts_header_from_chrom_sizes(const std::vector<std::string> &chrom_names,
+                                     const std::vector<uint64_t> &chrom_sizes,
+                                     bamxx::bgzf_file &out);
 
 // returns -1 on failure, 0 on success
 int

src/utils/xcounts.cpp

@@ -1,5 +1,5 @@
 /* xcounts: reformat counts so they only give the m and u counts in a
- * wig format
+ * dynamic step wig format
  *
  * Copyright (C) 2023 Andrew D. Smith
  *
@@ -145,14 +145,13 @@ main_xcounts(int argc, const char **argv) {
     if (!out) throw dnmt_error("error opening output file: " + outfile);
 
     if (n_threads > 1) {
-      // ADS: something breaks when we use the thread for the input
       if (in.is_bgzf())
         tpool.set_io(in);
       tpool.set_io(out);
     }
 
     if (!genome_file.empty())
-      write_counts_header_from_chom_sizes(chrom_names, chrom_sizes, out);
+      write_counts_header_from_chrom_sizes(chrom_names, chrom_sizes, out);
 
     // use the kstring_t type to more directly use the BGZF file
     kstring_t line{0, 0, nullptr};