Merge pull request #224 from smithlabcode/fixing-malformed-usage-mess…

…ages fixing malformed usage messages
smithlabcode · Jun 7, 2024 · 72e0376 · 72e0376
2 parents 94c219f + 19116b3
commit 72e0376
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Showing 2 changed files with 7 additions and 9 deletions.
diff --git a/src/dnmtools.cpp b/src/dnmtools.cpp
@@ -173,9 +173,9 @@ main(int argc, const char **argv) {
    {"hmr-rep",   "identify hypomethylated regions in a set of replicate methylomes", main_hmr_rep},
    {"hypermr",   "identify hypermethylated regions in plant methylomes", main_hypermr},
    {"entropy",   "compute methylation entropy in sliding window", main_methentropy},
-   {"multistat", "summarize methylation from to genomic intervals in a BED file", main_multimethstat},
    {"pmd",       "identify partially methylated domains", main_pmd},
-   {"roi",       "compute average CpG methylation in each of a set of genomic interval", main_roimethstat},
+   {"roi",       "get average CpG methylation in each of a set of genomic interval", main_roimethstat},
+   {"multistat", "same as roi except for multiple samples/input files", main_multimethstat},
    {"mlml",      "program to estimate hydroxymethylation levels", main_mlml}}}},
 
 {"allele-specific methylation (ASM)",

diff --git a/src/utils/merge-methcounts.cpp b/src/utils/merge-methcounts.cpp
@@ -373,12 +373,11 @@ main_merge_methcounts(int argc, const char **argv) {
                       false, header_info);
     opt_parse.add_opt("tabular", 't', "output as table",
                       false, write_tabular_format);
-    opt_parse.add_opt("radmeth", '\0', "Format header for radmeth "
-                      "(assumes -tabular and not -fractional)",
+    opt_parse.add_opt("radmeth", '\0', "make radmeth input "
+                      "(use with tabular and without fractional)",
                       false, radmeth_format);
-    opt_parse.add_opt("remove", '\0', "Suffix to remove from filenames when "
-                      "making column names for tabular format. If not "
-                      "specified, suffix including from final dot is removed.",
+    opt_parse.add_opt("remove", '\0', "remove this suffix from filenames when "
+                      "making column names; default removes from final dot",
                       false, suffix_to_remove);
     opt_parse.add_opt("suff", 's',
                       "column name suffixes, one for total reads and one for "
@@ -395,8 +394,7 @@ main_merge_methcounts(int argc, const char **argv) {
     opt_parse.add_opt("mut", 'm',"If any of the sites being merged indicates "
                       "mutated, mark the result has mutated.",
                       false, report_any_mutated);
-    opt_parse.add_opt("first-column-header", '\0',"Add a header for the first "
-                      "to support reading the table using various other tools",
+    opt_parse.add_opt("1st-col-header", '\0',"add name for 1st col in header",
                       false, add_first_column_header);
     opt_parse.add_opt("verbose", 'v',"print more run info", false, VERBOSE);
     opt_parse.set_show_defaults();