Remove or add back non-covered sites from compressed counts files

Makefile.am

@@ -214,6 +214,8 @@ dnmtools_SOURCES += src/utils/symmetric-cpgs.cpp
 dnmtools_SOURCES += src/utils/merge-methcounts.cpp
 dnmtools_SOURCES += src/utils/lift-filter.cpp
 dnmtools_SOURCES += src/utils/fast-liftover.cpp
+dnmtools_SOURCES += src/utils/covered.cpp
+dnmtools_SOURCES += src/utils/recovered.cpp
 dnmtools_SOURCES += src/utils/kmersites.cpp
 
 dnmtools_SOURCES += src/amrfinder/allelicmeth.cpp

src/dnmtools.cpp

@@ -126,6 +126,10 @@ main_symmetric_cpgs(int argc, const char **argv);
 int
 metagene(int argc, const char **argv);
 int
+main_covered(int argc, const char **argv);
+int
+main_recovered(int argc, const char **argv);
+int
 kmersites(int argc, const char **argv);
 
 void
@@ -194,6 +198,8 @@ main(int argc, const char **argv) {
    {"lc",            "approximate line counts in a file", main_lc_approx},
    {"merge-bsrate",  "merge bisulfite conversion rates files from bsrate", main_merge_bsrate},
    {"merge",         "merge multiple counts files into a counts file or a table", main_merge_methcounts},
+   {"covered",       "filter a counts file for only covered sites", main_covered},
+   {"recovered",     "replace missing sites in a counts file", main_recovered},
    {"selectsites",   "sites inside a set of genomic intervals", main_selectsites},
    {"kmersites",     "make track file for sites matching kmer", kmersites}}}}}};
 // clang-format on

src/utils/covered.cpp

@@ -0,0 +1,100 @@
+/* covered: filter counts files so they only have covered sites.
+ *
+ * Copyright (C) 2023 Andrew D. Smith
+ *
+ * Authors: Andrew D. Smith
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * General Public License for more details.
+ */
+
+#include <string>
+#include <vector>
+#include <iostream>
+#include <stdexcept>
+#include <bamxx.hpp>
+
+// from smithlab_cpp
+#include "OptionParser.hpp"
+#include "smithlab_utils.hpp"
+#include "smithlab_os.hpp"
+
+#include "MSite.hpp"
+
+using std::string;
+using std::cout;
+using std::cerr;
+using std::endl;
+
+using bamxx::bgzf_file;
+
+int
+main_covered(int argc, const char **argv) {
+  try {
+
+    size_t n_threads = 1;
+
+    string outfile;
+    const string description =
+      "filter counts files so they only have covered sites";
+
+    /****************** COMMAND LINE OPTIONS ********************/
+    OptionParser opt_parse(strip_path(argv[0]), description,
+                           "<methcounts-file>");
+    opt_parse.add_opt("output", 'o', "output file (required)", true, outfile);
+    opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
+    std::vector<string> leftover_args;
+    opt_parse.parse(argc, argv, leftover_args);
+    if (argc == 1 || opt_parse.help_requested()) {
+      cerr << opt_parse.help_message() << endl
+           << opt_parse.about_message() << endl;
+      return EXIT_SUCCESS;
+    }
+    if (opt_parse.about_requested()) {
+      cerr << opt_parse.about_message() << endl;
+      return EXIT_SUCCESS;
+    }
+    if (opt_parse.option_missing()) {
+      cerr << opt_parse.option_missing_message() << endl;
+      return EXIT_SUCCESS;
+    }
+    if (leftover_args.size() != 1) {
+      cerr << opt_parse.help_message() << endl;
+      return EXIT_SUCCESS;
+    }
+    const string filename(leftover_args.front());
+    /****************** END COMMAND LINE OPTIONS *****************/
+
+    bamxx::bam_tpool tpool(n_threads);
+
+    // const bool show_progress = VERBOSE && isatty(fileno(stderr));
+    bgzf_file in(filename, "r");
+    if (!in) throw std::runtime_error("could not open file: " + filename);
+
+    // open the output file
+    bamxx::bgzf_file out(outfile, "w");
+    if (!out) throw std::runtime_error("error opening output file: " + outfile);
+
+    if (n_threads > 1) {
+      tpool.set_io(in);
+      tpool.set_io(out);
+    }
+
+    MSite site;
+    while (read_site(in, site)) 
+      if (site.n_reads > 0 || site.is_mutated()) 
+        write_site(out, site);
+  }
+  catch (const std::runtime_error &e) {
+    cerr << e.what() << endl;
+    return EXIT_FAILURE;
+  }
+  return EXIT_SUCCESS;
+}