fixing conflicts in xcounts.cpp when merging from master

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.hpp

@@ -31,7 +31,7 @@ write_counts_header_from_chrom_sizes(const std::vector<std::string> &chrom_names
                                      bamxx::bgzf_file &out);
 
 void
-write_counts_header_from_file(const std::string &header_file, 
+write_counts_header_from_file(const std::string &header_file,
                               bamxx::bgzf_file &out);
 
 // returns -1 on failure, 0 on success

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
  *
@@ -148,7 +148,6 @@ 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);