multiple sources: making output file a required argument

Author: andrewdavidsmith

src/amrfinder/allelicmeth.cpp

@@ -234,8 +234,7 @@ computes probability of allele-specific methylation at each tuple of CpGs
     /****************** COMMAND LINE OPTIONS ********************/
     OptionParser opt_parse(argv[0],  // NOLINT(*-pointer-arithmetic)
                            description, "<epireads>");
-    opt_parse.add_opt("output", 'o', "output file name (default: stdout)",
-                      false, outfile);
+    opt_parse.add_opt("output", 'o', "output file name", true, outfile);
     opt_parse.add_opt("chrom", 'c', "genome sequence file/directory", true,
                       chroms_dir);
     opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);

src/amrfinder/amrtester.cpp

@@ -193,7 +193,7 @@ main_amrtester(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
     OptionParser opt_parse(argv[0],  // NOLINT(*-pointer-arithmetic)
                            "resolve epi-alleles",
                            "<bed-regions> <mapped-reads>");
-    opt_parse.add_opt("output", 'o', "output file", false, outfile);
+    opt_parse.add_opt("output", 'o', "output file", true, outfile);
     opt_parse.add_opt("chrom", 'c', "reference genome fasta file", true,
                       chrom_file);
     opt_parse.add_opt("itr", 'i', "max iterations", false, max_itr);

src/analysis/cpgbins.cpp

@@ -195,8 +195,7 @@ Columns (beyond the first 6) in the BED format output:
     OptionParser opt_parse(argv[0],  // NOLINT(*-pointer-arithmetic)
                            description, "<chrom-sizes> <xsym-file>");
     opt_parse.set_show_defaults();
-    opt_parse.add_opt("output", 'o', "name of output file (default: stdout)",
-                      true, outfile);
+    opt_parse.add_opt("output", 'o', "name of output file", true, outfile);
     opt_parse.add_opt("bin", 'b', "bin size in base pairs", false, bin_size);
     opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
     opt_parse.add_opt("level", 'l',

src/analysis/hmr-rep.cpp

@@ -348,8 +348,7 @@ main_hmr_rep(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
     OptionParser opt_parse(argv[0],  // NOLINT(*-pointer-arithmetic)
                            description,
                            "<methcount-file-1> <methcount-file-2> ...");
-    opt_parse.add_opt("out", 'o', "output file (default: stdout)", false,
-                      outfile);
+    opt_parse.add_opt("out", 'o', "output file", true, outfile);
     opt_parse.add_opt("desert", 'd', "max dist btwn cpgs with reads in HMR",
                       false, desert_size);
     opt_parse.add_opt("itr", 'i', "max iterations", false, max_iterations);

src/analysis/hypermr.cpp

@@ -243,7 +243,7 @@ main_hypermr(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
     /****************** COMMAND LINE OPTIONS ********************/
     OptionParser opt_parse(argv[0],  // NOLINT(*-pointer-arithmetic)
                            about, "<counts-file>");
-    opt_parse.add_opt("out", 'o', "output file (BED format)", false, outfile);
+    opt_parse.add_opt("out", 'o', "output file", true, outfile);
     opt_parse.add_opt("scores", 's', "output file for posterior scores", false,
                       scores_file);
     opt_parse.add_opt("tolerance", 't', "numerical tolerance", false,

src/analysis/metagene.cpp

@@ -112,8 +112,7 @@ correctly.
     /****************** GET COMMAND LINE ARGUMENTS ***************************/
     OptionParser opt_parse(argv[0],  // NOLINT(*-pointer-arithmetic)
                            description, "<features-bed> <counts>");
-    opt_parse.add_opt("output", 'o', "output file (default: terminal)", false,
-                      outfile);
+    opt_parse.add_opt("output", 'o', "output file", true, outfile);
     opt_parse.add_opt("size", 's', "analyze this size in both directions",
                       false, region_size);
     opt_parse.add_opt("bin", 'b', "bin size", false, bin_size);

src/analysis/multimethstat.cpp

@@ -510,8 +510,7 @@ main_multimethstat(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
                            "methylation in each of a set of genomic intervals",
                            "<intervals-bed> <methylation-file>");
     opt_parse.set_show_defaults();
-    opt_parse.add_opt("output", 'o', "Name of output file (default: stdout)",
-                      false, outfile);
+    opt_parse.add_opt("output", 'o', "output file", true, outfile);
     opt_parse.add_opt("numeric", 'N', "print numeric values only (not NAs)",
                       false, print_numeric_only);
     opt_parse.add_opt("preload", 'L', "Load all CpG sites", false,

src/analysis/pmd.cpp

@@ -1135,8 +1135,7 @@ main_pmd(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
     /****************** COMMAND LINE OPTIONS ********************/
     OptionParser opt_parse(argv[0],  // NOLINT(*-pointer-arithmetic)
                            description, "<methcount-files>");
-    opt_parse.add_opt("out", 'o', "output file (default: stdout)", false,
-                      outfile);
+    opt_parse.add_opt("out", 'o', "output file", true, outfile);
     opt_parse.add_opt("desert", 'd', "max dist between bins with data in PMD",
                       false, desert_size);
     opt_parse.add_opt("fixedbin", 'f', "Fixed bin size", false, fixed_bin_size);

src/analysis/roimethstat.cpp

@@ -421,7 +421,7 @@ Columns (beyond the first 6) in the BED format output:
     OptionParser opt_parse(argv[0],  // NOLINT(*-pointer-arithmetic)
                            description, "<intervals-bed> <methylation-file>");
     opt_parse.set_show_defaults();
-    opt_parse.add_opt("output", 'o', "Name of output file", true, outfile);
+    opt_parse.add_opt("output", 'o', "output file", true, outfile);
     opt_parse.add_opt("numeric", 'N', "print numeric values only (not NAs)",
                       false, print_numeric_only);
     opt_parse.add_opt("preload", 'L', "load all site sites", false, preload);

src/radmeth/radmeth-merge.cpp

@@ -143,8 +143,7 @@ main_radmeth_merge(int argc, char *argv[]) {  // NOLINT(*-avoid-c-arrays)
                            " methylated CpGs into DMRs",
                            "<bed-file-in-radmeth-format>");
     opt_parse.set_show_defaults();
-    opt_parse.add_opt("output", 'o', "output file (default: stdout)", false,
-                      outfile);
+    opt_parse.add_opt("output", 'o', "output file", true, outfile);
     opt_parse.add_opt("cutoff", 'p', "p-value cutoff", false, cutoff);
     std::vector<std::string> leftover_args;
     opt_parse.parse(argc, argv, leftover_args);