unified options for summary for pmd, hmr, and uniq

Author: masarunakajima

docs/content/hmr.md

@@ -172,7 +172,7 @@ to filering candidate HMRs. This parameter is typically only used for
 testing (default: 408).
 
 ```txt
- -summary
+ -S, -summary
 ```
 Write the analysis summary to this file. The summary is not
-reported unless a file is specified here.
+reported unless a file is specified here. This option is correct as of v1.4.0.

docs/content/pmd.md

@@ -188,8 +188,8 @@ Write the trained parameters to this file.
 Specify a random seed value.
 
 ```txt
- -summary
+ -S, -summary
 ```
 Write the analysis summary to this file. The summary is not
-reported unless a file is specified here.
+reported unless a file is specified here. This option is correct as of v1.4.0.
 

docs/content/uniq.md

@@ -49,10 +49,10 @@ most helpful when the input and output are both BAM, where the threads
 can really speed things up.
 
 ```txt
- -S, -stats
+ -S, -summary
 ```
 Save statistics on duplication rates to this file. The statistics are not
-reported unless a file is specified here.
+reported unless a file is specified here. This option is correct as of v1.4.0.
 
 ```txt
  -hist

src/analysis/hmr.cpp

@@ -452,7 +452,7 @@ main_hmr(int argc, const char **argv) {
     opt_parse.add_opt("params-out", 'p', "write HMM parameters to this "
                       "file (default: none)", false, params_out_file);
     opt_parse.add_opt("seed", 's', "specify random seed", false, rng_seed);
-    opt_parse.add_opt("summary", '\0', "write summary output here", false, 
+    opt_parse.add_opt("summary", 'S', "write summary output here", false, 
                       summary_file);
     opt_parse.set_show_defaults();
     vector<string> leftover_args;

src/analysis/pmd.cpp

@@ -1168,7 +1168,7 @@ main_pmd(int argc, const char **argv) {
     opt_parse.add_opt("posteriors-out", 'r',
                       "write out posterior probabilities in methcounts format",
                       false, posteriors_out_prefix);
-    opt_parse.add_opt("summary", '\0',
+    opt_parse.add_opt("summary", 'S',
                       "write summary output here",
                       false, summary_file);
     opt_parse.add_opt("params-out", 'p', "write HMM parameters to this file",

src/utils/uniq.cpp

@@ -286,7 +286,7 @@ main_uniq(int argc, const char **argv) {
                            "sorted mapped reads",
                            "<in-file> [out-file]", 2);
     opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
-    opt_parse.add_opt("stats", 'S', "statistics output file", false, statfile);
+    opt_parse.add_opt("summary", 'S', "statistics output file", false, statfile);
     opt_parse.add_opt("add-count", 'a', "add duplicate counts to reads", false,
                       add_dup_count);
     opt_parse.add_opt("hist", '\0',