Refine Tajima D policy help text and order

src/commands/analyze/diversity.cpp

@@ -109,15 +109,6 @@ void setup_diversity( CLI::App& app )
     // );
     // options->no_nan_windows.option->group( "Settings" );
 
-    // PoPoolation output format
-    options->popoolation_format.option = sub->add_flag(
-        "--popoolation-format",
-        options->popoolation_format.value,
-        "If set, instead of writing one output table for all measures and all samples, "
-        "write the results in separate files for each sample and for each measure of "
-        "Theta Pi, Theta Watterson, and Tajima's D, following the format of PoPoolation."
-    )->group( "Settings" );
-
     // -------------------------------------------------------------------------
     //     Output
     // -------------------------------------------------------------------------
@@ -126,6 +117,15 @@ void setup_diversity( CLI::App& app )
     auto sep_opt = options->table_output.add_separator_char_opt_to_app( sub );
     auto nan_opt = options->table_output.add_na_entry_opt_to_app( sub );
 
+    // PoPoolation output format
+    options->popoolation_format.option = sub->add_flag(
+        "--popoolation-format",
+        options->popoolation_format.value,
+        "If set, instead of writing one output table for all measures and all samples, "
+        "write the results in separate files for each sample and for each measure of "
+        "Theta Pi, Theta Watterson, and Tajima's D, following the format of PoPoolation."
+    )->group( "Formatting" );
+
     // Exclude separator char option and na entry in PoPoolation compatibility mode,
     // as we have to use their values in that case.
     sep_opt->excludes( options->popoolation_format.option );

src/options/diversity_processor.cpp

@@ -88,18 +88,18 @@ void DiversityProcessorOptions::add_diversity_processor_opts_to_app(
         "With pool seq data, there is no simple way to obtain a statistic that is numerically "
         "comparable to the classic Tajima's D with individual data. Hence, all of the below are "
         "simplicications that introduce some bias."
-        "\n(1) Empirical minimum read depth: Use the lowest empirical read depth found in each window, "
+        "\n(1) `empirical-min-read-depth`: Use the lowest empirical read depth found in each window, "
         "and the pool size, to compute the expected number of individuals sequenced. "
         "This is a conservative estimator that we recommend by default."
-        "\n(2) User-provided minimum read depth: Same as (1), but use the "
+        "\n(2) `provided-min-read-depth`: Same as (1), but use the user-provided "
         "`--filter-sample-min-read-depth` instead of the empirical minum read depth. "
         "This is what PoPoolation uses."
-        "\n(3) PoPoolation bugs: Same as (2), but additionally re-introduce their bugs. "
+        "\n(3) `popoolation-bugs`: Same as (2), but additionally re-introduce their bugs. "
         "We offer this for comparability with PoPoolation."
-        "\n(4) Pool size: Directly use the pool size as an estimate of the number of individuals, "
+        "\n(4) `pool-size`: Directly use the pool size as an estimate of the number of individuals, "
         "instead of computing the expected value. This assumes the number of individuals sequenced "
         "to be equal to the pool size, and is good under high read depths."
-        "\n(5) Uncorrected: The Achaz correction is not applied, so that the result is simply "
+        "\n(5) `uncorrected`: The Achaz correction is not applied, so that the result is simply "
         "Theta Pi minus Theta Watterson. Hence, magnitudes of values are not comparable to classic "
         "Tajima's D. Still, using their sign, and comparing them across windows can be useful."
     );