Move default consensus slack to SalmonDefaults

- Fix the message to the user about how the default consensus slack is being set. This should address #587.
COMBINE-lab · Nov 20, 2020 · 54a4cf1 · 54a4cf1
1 parent cf3ff50
commit 54a4cf1
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/include/SalmonDefaults.hpp b/include/SalmonDefaults.hpp
@@ -22,7 +22,7 @@ namespace defaults {
   // advanced
   constexpr const bool validateMappings{true};
   constexpr const bool disableSA{false};
-  constexpr const float consensusSlack{0.0};
+  constexpr const float consensusSlack{0.35};
   constexpr const double minScoreFraction{0.65};
   constexpr const double pre_merge_chain_sub_thresh{0.75};
   constexpr const double post_merge_chain_sub_thresh{0.9};

diff --git a/src/SalmonUtils.cpp b/src/SalmonUtils.cpp
@@ -1515,10 +1515,9 @@ std::string getCurrentTimeAsString() {
     // validateMappings
     bool consensusSlackExplicit = !vm["consensusSlack"].defaulted();
     if (!consensusSlackExplicit) {
-      sopt.consensusSlack = 0.35;
       sopt.jointLog->info(
-                          "Usage of --validateMappings implies a default consensus slack of 0.2. "
-                          "Setting consensusSlack to {}.", sopt.consensusSlack);
+                          "Setting consensusSlack to selective-alignment default of {}.", 
+                          sopt.consensusSlack);
     }
 
     bool pre_merge_chain_sub_thresh_explicit = !vm["preMergeChainSubThresh"].defaulted();