add different secondary mapping count for seqs less than segLength

This helps us to map collections of reads with different sizes, where
some are below the desired segment length for the entire collection. We
can still use these sequences, but we might not want to map them many
places. This makes that configurable, so by default we at least align
them to their best mapping, but we can potentially multi-map too.

src/map/include/computeMap.hpp

@@ -152,7 +152,7 @@ namespace skch
                     if (param.filterMode == filter::ONETOONE)
                         qmetadata.push_back( ContigInfo{seq_name, len} );
                     //Is the read too short?
-                    if(len < param.windowSize || len < param.kmerSize || len < param.segLength)
+                    if(len < param.windowSize || len < param.kmerSize)
                     {
 //#ifdef DEBUG
                         std::cerr << "WARNING, skch::Map::mapQuery, read is not long enough for mapping" << std::endl;
@@ -215,7 +215,7 @@ namespace skch
         //save query sequence name
         output->qseqName = input->seqName;
 
-        if(! param.split)   
+        if(! param.split || input->len <= param.segLength)
         {
           QueryMetaData <MinVec_Type> Q;
           Q.seq = &(input->seq)[0u];
@@ -294,7 +294,10 @@ namespace skch
         //filter mappings best over query sequence axis
         if(param.filterMode == filter::MAP || param.filterMode == filter::ONETOONE)
         {
-            skch::Filter::query::filterMappings(output->readMappings, param.secondaryToKeep);
+            skch::Filter::query::filterMappings(output->readMappings,
+                                                (input->len < param.segLength ?
+                                                 param.shortSecondaryToKeep
+                                                 : param.secondaryToKeep));
         }
 
         //Make sure mapping boundary don't exceed sequence lengths

src/map/include/map_parameters.hpp

@@ -26,6 +26,7 @@ struct Parameters
     float percentageIdentity;                         //user defined threshold for good similarity
     int filterMode;                                   //filtering mode in mashmap
     int secondaryToKeep;                              //how many secondary alignments we keep
+    int shortSecondaryToKeep;                         //how many secondary alignments we keep for reads < segLength
     int threads;                                      //execution thread count
     std::vector<std::string> refSequences;            //reference sequence(s)
     std::vector<std::string> querySequences;          //query sequence(s)

src/yeet/include/parse_args.hpp

@@ -40,6 +40,7 @@ void parse_args(int argc,
     args::ValueFlag<int> kmer_size(parser, "N", "kmer size <= 16 [default: 16]", {'k', "kmer"});
     args::ValueFlag<std::string> map_filter_mode(parser, "MODE", "filter mode for map step, either 'map', 'one-to-one', or 'none' [default: map]", {'f', "map-filter-mode"});
     args::ValueFlag<int> map_secondaries(parser, "N", "number of secondary mappings to retain in 'map' filter mode (total number of mappings is this + 1) [default: 0]", {'n', "n-secondary"});
+    args::ValueFlag<int> map_short_secondaries(parser, "N", "number of secondary mappings to retain for sequences shorter than segment length [default: 0]", {'S', "n-short-secondary"});
     args::Flag skip_self(parser, "", "skip self mappings when the query and target name is the same (for all-vs-all mode)", {'X', "skip-self"});
     args::ValueFlag<char> skip_prefix(parser, "C", "skip mappings when the query and target have the same prefix before the given character C", {'Y', "skip-prefix"});
     args::Flag approx_mapping(parser, "approx-map", "skip base-level alignment, producing an approximate mapping in PAF", {'m',"approx-map"});
@@ -218,6 +219,12 @@ void parse_args(int argc,
         map_parameters.secondaryToKeep = 0;
     }
 
+    if (map_short_secondaries) {
+        map_parameters.shortSecondaryToKeep = args::get(map_short_secondaries);
+    } else {
+        map_parameters.shortSecondaryToKeep = 0;
+    }
+
     if (skip_self) {
         map_parameters.skip_self = true;
     } else {