Correct warning bounds for hg filter

marbl · Aug 19, 2023 · 93d12ad · 93d12ad
1 parent 565756b
commit 93d12ad
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/src/map/include/parseCmdArgs.hpp b/src/map/include/parseCmdArgs.hpp
@@ -102,7 +102,7 @@ sequences shorter than segment length will be ignored", ArgvParser::OptionRequir
 
     cmd.defineOption("noHgFilter", "Don't use the hypergeometric filtering and instead use the MashMap2 first pass filtering.");
     cmd.defineOption("hgFilterAniDiff", "Filter out mappings unlikely to be this ANI less than the best mapping [default: 0.0]", ArgvParser::OptionRequiresValue);
-    cmd.defineOption("hgFilterConf", "Confidence value for the hypergeometric filtering [default: 0.999]", ArgvParser::OptionRequiresValue);
+    cmd.defineOption("hgFilterConf", "Confidence value for the hypergeometric filtering [default: 99.9%]", ArgvParser::OptionRequiresValue);
 
     cmd.defineOption("filterLengthMismatches", "Filter mappings where the ratio of reference/query mapped lengths disagrees with the ANI threshold");
 
@@ -564,11 +564,11 @@ sequences shorter than segment length will be ignored", ArgvParser::OptionRequir
     if (cmd.foundOption("hgFilterAniDiff")) {
       str << cmd.optionValue("hgFilterAniDiff");
       str >> parameters.ANIDiff;
-      parameters.ANIDiff /= 100;
       if (parameters.ANIDiff < 0 ||  parameters.ANIDiff > 100) {
         std::cerr << "ERROR, skch::parseandSave, ANI difference must be between 0 and 100" << std::endl;
         exit(1);
       }
+      parameters.ANIDiff /= 100;
     } else {
       parameters.ANIDiff = skch::fixed::ANIDiff;
     }
@@ -577,11 +577,11 @@ sequences shorter than segment length will be ignored", ArgvParser::OptionRequir
     if (cmd.foundOption("hgFilterConf")) {
       str << cmd.optionValue("hgFilterConf");
       str >> parameters.ANIDiffConf;
-      parameters.ANIDiffConf /= 100;
-      if (parameters.ANIDiffConf < 0 ||  parameters.ANIDiffConf > 1) {
-        std::cerr << "ERROR, skch::parseandSave, hypergeometric confidence must be between 0 and 1" << std::endl;
+      if (parameters.ANIDiffConf < 0 ||  parameters.ANIDiffConf > 100) {
+        std::cerr << "ERROR, skch::parseandSave, hypergeometric confidence must be between 0 and 100" << std::endl;
         exit(1);
       }
+      parameters.ANIDiffConf /= 100;
     } else {
       parameters.ANIDiffConf = skch::fixed::ANIDiffConf;
     }