Merge pull request #269 from ASLeonard/main

smooth the introduction of max mapping length parameter
waveygang · Sep 20, 2024 · 1f485f3 · 1f485f3
2 parents b731e41 + c48e848
commit 1f485f3
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diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp
@@ -440,6 +440,11 @@ void parse_args(int argc,
         map_parameters.max_mapping_length = 50000;
     }
 
+    if (map_parameters.segLength >= map_parameters.max_mapping_length) {
+        std::cerr << "[wfmash] ERROR, skch::parseandSave, segment length should not be larger than max mapping length." << std::endl;
+        exit(1);
+    }
+
     if (drop_low_map_pct_identity) {
         map_parameters.keep_low_pct_id = false;
     } else {

diff --git a/src/map/include/parseCmdArgs.hpp b/src/map/include/parseCmdArgs.hpp
@@ -223,6 +223,7 @@ sequences shorter than segment length will be ignored", ArgvParser::OptionRequir
 
     }
     std::cerr << "[mashmap] Chaining gap max = " << parameters.chain_gap << std::endl;
+    std::cerr << "[mashmap] Max mapping length = " << parameters.max_mapping_length << std::endl;
     std::cerr << "[mashmap] Mappings per segment = " << parameters.numMappingsForSegment << std::endl;
     std::cerr << "[mashmap] Percentage identity threshold = " << 100 * parameters.percentageIdentity << "\%" << std::endl;