From 8b479b817d4af43a482dfe166c9edfd281e00a33 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 6 Jun 2024 17:46:39 -0700 Subject: [PATCH 1/2] merge: fixing some cli descriptions --- src/utils/merge-methcounts.cpp | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/src/utils/merge-methcounts.cpp b/src/utils/merge-methcounts.cpp index a2ee3b5d..c597aa09 100644 --- 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(); From 19116b34b658f18d5dcd0f22ba67f91da7a6eb47 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 6 Jun 2024 17:46:51 -0700 Subject: [PATCH 2/2] src/dnmtools.cpp: fixing a cli description --- src/dnmtools.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/dnmtools.cpp b/src/dnmtools.cpp index f2aae2f6..02cb9ca1 100644 --- 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)",