Merge pull request #1454 from veg/develop

v2.3.36 RC

CMakeLists.txt

@@ -53,10 +53,6 @@ macro(PCL_CHECK_FOR_NEON)
 	  include(CheckCXXSourceRuns)
 	  set(CMAKE_REQUIRED_FLAGS)
 
-	  #if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
-		  set(CMAKE_REQUIRED_FLAGS "-msse3")
-	  #endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
-
 	  check_cxx_source_runs("
 		#include <stdio.h>
 		#include <arm_neon.h>
@@ -213,6 +209,13 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
         endif(${HAVE_AVX_EXTENSIONS})
     endif(NOAVX)
 
+	if(NOT NONEON)
+		PCL_CHECK_FOR_NEON()
+		if(${HAVE_NEON_EXTENSIONS})
+			add_definitions (-D_SLKP_USE_ARM_NEON)
+		endif(${HAVE_NEON_EXTENSIONS})
+	endif(NOT NONEON)
+
 
     set(DEFAULT_LINK_FLAGS "${DEFAULT_COMPILE_FLAGS}")
 endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)

res/TemplateBatchFiles/BGM.bf

@@ -107,7 +107,11 @@ selection.io.json_store_key_value_pair (bgm.json, terms.json.input, terms.json.s
 selection.io.json_store_key_value_pair (bgm.json, terms.json.input, terms.json.sites, bgm.alignment_info [terms.data.sites]);
 selection.io.json_store_key_value_pair (bgm.json, terms.json.input, terms.data_type, bgm.type);
 
+
+
 bgm.alignment_info[terms.json.json] = bgm.alignment_info[terms.data.file] + ".BGM.json";
+KeywordArgument ("output", "Write the resulting JSON to this file (default is to save to the same path as the alignment file + 'FEL.json')", bgm.alignment_info [terms.json.json]);
+bgm.alignment_info [terms.json.json] = io.PromptUserForFilePath ("Save the resulting JSON file to");
 
 bgm.path.base = (bgm.json [terms.json.input])[terms.json.file];
 
@@ -144,14 +148,18 @@ KeywordArgument ("steps", "The number of MCMC steps to sample", 100000);
 KeywordArgument ("burn-in", "The number of MCMC steps to discard as burn-in", 10000);
 KeywordArgument ("samples", "The number of steps to extract from the chain sample", 100);
 KeywordArgument ("max-parents", "The maximum number of parents allowed per node", 1);
-KeywordArgument ("min-subs", "The minium number of substitutions per site to include it in the analysis", 1);
+KeywordArgument ("min-subs", "The minimum number of substitutions per site to include it in the analysis", 1);
 
 
 bgm.run_settings["steps"]      = io.PromptUser("\n>Select the number of MCMC steps to sample", bgm.run_settings["steps"] , 0, 1e9, TRUE);
+
 bgm.run_settings["burn-in"]      = io.PromptUser("\n>Select the number of MCMC steps to discard as burn-in", bgm.run_settings["burn-in"], 0, 1e9, TRUE);
-bgm.run_settings["samples"]    = io.PromptUser("\n>Select the number of steps to extract from the chain sample", 100, 0, bgm.run_settings["samples"], TRUE);
+
+bgm.run_settings["samples"]    = io.PromptUser("\n>Select the number of steps to extract from the chain sample", bgm.run_settings["samples"], 100,  bgm.run_settings["steps"] - bgm.run_settings["burn-in"],  TRUE);
+
 bgm.run_settings["max-parents"] = io.PromptUser ("\n>Select the maximum number of parents allowed per node", bgm.run_settings["max-parents"], 1, 3, TRUE);
-bgm.run_settings["min-subs"]    = io.PromptUser ("\n>Select the minium number of substitutions per site to include it in the analysis", bgm.run_settings["min-subs"], 1, 1e5, TRUE);
+
+bgm.run_settings["min-subs"]    = io.PromptUser ("\n>Select the minimum number of substitutions per site to include it in the analysis", bgm.run_settings["min-subs"], 1, 1e5, TRUE);
 
 
 // FIT THE BASELINE MODEL
@@ -357,6 +365,8 @@ selection.io.stopTimer (bgm.json [terms.json.timers], "Overall");
 
 bgm.json [terms.settings] = bgm.run_settings;
 
+
+
 io.SpoolJSON (bgm.json, bgm.alignment_info[terms.json.json]);