Removed unused --steps option in neoscan.

src/lib/jade.version.hpp

@@ -30,7 +30,7 @@ namespace jade
                 char_type const * const title, ///< The program name.
                 ostream_type &          out)   ///< The output stream.
         {
-            static const values current { 0, 0, 6416, 42877, 2015, 2017 };
+            static const values current { 0, 0, 6416, 43183, 2015, 2017 };
 
             out << "ohana/" << title << ' '
                 << current.major << '.'

src/neoscan/jade.main.cpp

@@ -19,14 +19,13 @@ ARGUMENTS
   year-matrix    path to the [I x 1] matrix for years
 
 OPTIONS
-  --steps,-s (30)   the number of steps to interpolate
-  --help,-h         shows this help message and exits
+  --help,-h      shows this help message and exits
 
 DESCRIPTION
   Performs a selection scan between ancient and modern data. The program can
   take advantage of the dating for each individual ancient sample. The program
-  prints for each marker the step number when local optima is reached, the
-  global likelihood, the optimal local likelihood, and the likelihood ratio.
+  prints for each marker the delta when local optima is reached, the global
+  likelihood, the optimal local likelihood, and the likelihood ratio.
 
   The program requires a <year-matrix>, which contains for each individual a
   row representing the number of years going backward in time. For instance,
@@ -36,7 +35,7 @@ DESCRIPTION
   [Notation]
 
   K := Number of Components
-     This value must be greater than or equal to two.
+     This value must be greater than or equal to one.
 
   I := Number of Individuals
      This value must be greater than or equal to two.
@@ -90,7 +89,7 @@ DESCRIPTION
   0.3  0.7  0.4  0.6
 
 EXAMPLE
-  $ neoscan --steps 3 g.dgm q.matrix f.matrix years.json
+  $ neoscan g.dgm q.matrix f.matrix years.json
   d       global-lle      local-lle       lle-ratio
   -1.00   +1.418028e+00   +1.418028e+00   +0.000000e+00
   +0.00   +1.769128e+00   +1.769128e+00   +0.000000e+00

src/neoscan/jade.neoscan.hpp

@@ -90,13 +90,11 @@ namespace jade
                 const genotype_matrix_type & g,     ///< The G matrix.
                 const matrix_type          & q,     ///< The Q matrix.
                 const matrix_type          & f,     ///< The F matrix.
-                const matrix_type          & years, ///< The years matrix.
-                const size_t                 steps) ///< The number of steps.
+                const matrix_type          & years) ///< The years matrix.
             : _g     (g)
             , _q     (q)
             , _f     (f)
             , _y     (_init_y(years, q))
-            , _steps (steps)
             , _f_j   (f.get_height(), 1)
         {
             verification_type::validate_gqf_sizes(g, q, f);
@@ -169,11 +167,6 @@ namespace jade
         ///
         static void run(args & a)
         {
-            const auto steps = a.read("--steps", "-s", size_t(30));
-            if (steps < 1)
-                throw jade::error()
-                    << "invalid number of steps (" << steps << ")";
-
             const std::unique_ptr<genotype_matrix_type> g_ptr (
                 genotype_matrix_factory_type::create(a.pop<std::string>()));
 
@@ -184,7 +177,7 @@ namespace jade
 
             std::cout << "d\tglobal_lle\tlocal_lle\tlle_ratio\n";
 
-            const basic_neoscan neoscan (*g_ptr, q, f, y, steps);
+            const basic_neoscan neoscan (*g_ptr, q, f, y);
 
             neoscan.execute([](const output & out)
             {
@@ -389,7 +382,6 @@ namespace jade
         const matrix_type          & _q;     // [I x K]
         const matrix_type          & _f;     // [K x J]
         const matrix_type            _y;     // [I x 1]
-        const size_t                 _steps;
 
         // scratch space
         mutable matrix_type _f_j; // [K x 1]

test/neoscan/test.neoscan.cpp

@@ -64,7 +64,7 @@ namespace
         2.0
         )";
 
-    const auto expected_dgm_30 = []()
+    const auto expected_dgm = []()
     {
         queue_type out;
         out.push({ +6.400005e-01, -2.586994e+00, -1.735003e+00 });
@@ -74,7 +74,7 @@ namespace
         return out;
     }();
 
-    const auto expected_lgm_30 = []()
+    const auto expected_lgm = []()
     {
         queue_type out;
         out.push({ -1.999980e-01, -3.969019e-01, -1.667654e-01 });
@@ -96,9 +96,9 @@ namespace
         const matrix_type f (f_in);
         const matrix_type y (y_in);
 
-        neoscan_type neoscan (g, q, f, y, 30);
+        neoscan_type neoscan (g, q, f, y);
 
-        auto expected = expected_dgm_30;
+        auto expected = expected_dgm;
 
         neoscan.execute([&expected](const neoscan_type::output & actual)
         {
@@ -127,9 +127,9 @@ namespace
         const matrix_type f (f_in);
         const matrix_type y (y_in);
 
-        neoscan_type neoscan (g, q, f, y, 30);
+        neoscan_type neoscan (g, q, f, y);
 
-        auto expected = expected_lgm_30;
+        auto expected = expected_lgm;
 
         neoscan.execute([&expected](const neoscan_type::output & actual)
         {