Merge branch 'mashmap3'

marbl · May 18, 2023 · a14fc00 · a14fc00
2 parents c989c62 + 08b959d
commit a14fc00
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Showing 3 changed files with 11 additions and 3 deletions.
diff --git a/src/map/include/computeMap.hpp b/src/map/include/computeMap.hpp
@@ -1589,7 +1589,7 @@ namespace skch
 
           if (!param.legacy_output) 
           {
-            outstrm   << sep << e.conservedSketches
+            outstrm  << sep << e.conservedSketches
                      << sep << e.blockLength
                      << sep << fakeMapQ
                      << sep << "id:f:" << e.nucIdentity;

diff --git a/src/map/include/map_parameters.hpp b/src/map/include/map_parameters.hpp
@@ -89,7 +89,7 @@ float confidence_interval = 0.95;                   // Confidence interval to re
 float percentage_identity = 0.85;                   // Percent identity in the mapping step
 float ANIDiff = 0.0;                                // Stage 1 ANI diff threshold
 float ANIDiffConf = 0.999;                          // ANI diff confidence
-std::string VERSION = "3.0.3";                      // Version of MashMap
+std::string VERSION = "3.0.4";                      // Version of MashMap
 }
 }
 

diff --git a/src/map/include/parseCmdArgs.hpp b/src/map/include/parseCmdArgs.hpp
@@ -199,12 +199,20 @@ sequences shorter than segment length will be ignored", ArgvParser::OptionRequir
    */
   void printCmdOptions(skch::Parameters &parameters)
   {
+    std::cerr << "[mashmap] MashMap v" << fixed::VERSION << std::endl;
     std::cerr << "[mashmap] Reference = " << parameters.refSequences << std::endl;
     std::cerr << "[mashmap] Query = " << parameters.querySequences << std::endl;
     std::cerr << "[mashmap] Kmer size = " << parameters.kmerSize << std::endl;
     std::cerr << "[mashmap] Sketch size = " << parameters.sketchSize << std::endl;
     std::cerr << "[mashmap] Segment length = " << parameters.segLength << (parameters.split ? " (read split allowed)": " (read split disabled)") << std::endl;
-    std::cerr << "[mashmap] Block length min = " << parameters.block_length << std::endl;
+    if (parameters.block_length <= parameters.segLength)
+    {
+      std::cerr << "[mashmap] No block length filtering" << std::endl;
+    } else
+    {
+      std::cerr << "[mashmap] Block length min = " << parameters.block_length << std::endl;
+
+    }
     std::cerr << "[mashmap] Chaining gap max = " << parameters.chain_gap << std::endl;
     std::cerr << "[mashmap] Mappings per segment = " << parameters.numMappingsForSegment << std::endl;
     std::cerr << "[mashmap] Percentage identity threshold = " << 100 * parameters.percentageIdentity << "\%" << std::endl;