Ensuring the VERSION is available for the PG lines in the SAM output. This is coming from the config.h file in the repo root, and might cause inconveniences for compiling and testing the tools without building the entire package

Author: andrewdavidsmith

src/utils/duplicate-remover.cpp

@@ -3,7 +3,7 @@
  * on identical mapping location and possibly also using the read
  * sequence if requested.
  *
- * Copyright (C) 2013-2021 University of Southern California and
+ * Copyright (C) 2013-2023 University of Southern California and
  *                         Andrew D. Smith
  *
  * Authors: Andrew D. Smith, Ben Decato, Song Qiang, Guilherme Sena
@@ -26,6 +26,8 @@
 #include <unordered_set>
 #include <stdexcept>
 
+#include <config.h>
+
 #include "OptionParser.hpp"
 #include "smithlab_utils.hpp"
 #include "smithlab_os.hpp"
@@ -374,11 +376,8 @@ main_duplicate_remover(int argc, const char **argv) {
     if (!out)
       throw runtime_error("failed to open output file: " + outfile);
 
-    // GS TODO: the empty argument below is the program version, it
-    // should be an extern string to the dnmtools version when we
-    // set prefix command calls
     std::ostringstream oss;
-    write_pg_line(argc, argv, "DUPLICATE_REMOVER", "", oss);
+    write_pg_line(argc, argv, "DUPLICATE_REMOVER", VERSION, oss);
     const string pg_line = oss.str();
 
     duplicate_remover(VERBOSE, USE_SEQUENCE, ALL_C, DISABLE_SORT_TEST,
@@ -388,9 +387,5 @@ main_duplicate_remover(int argc, const char **argv) {
     cerr << e.what() << endl;
     return EXIT_FAILURE;
   }
-  catch (std::bad_alloc &ba) {
-    cerr << "ERROR: could not allocate memory" << endl;
-    return EXIT_FAILURE;
-  }
   return EXIT_SUCCESS;
 }

src/utils/format-reads.cpp

@@ -36,7 +36,7 @@
 #include <cmath>
 #include <sstream>
 
-#include "config.h"
+#include <config.h>
 
 #include "OptionParser.hpp"
 #include "smithlab_utils.hpp"
@@ -442,9 +442,5 @@ main_format_reads(int argc, const char **argv) {
     cerr << e.what() << endl;
     return EXIT_FAILURE;
   }
-  catch (std::bad_alloc &ba) {
-    cerr << "ERROR: could not allocate memory" << endl;
-    return EXIT_FAILURE;
-  }
   return EXIT_SUCCESS;
 }