fix: update to newest fmindex_collection

- This also changes the way that a search with an reversed index is
working, so no reversing of the text is required anymore.

- Requires to set the numbers of thread used for suffix array
  construction.

Author: SGSSGene

src/mkindex_algo.hpp

@@ -603,7 +603,7 @@ auto generateIndex(TStringSet & seqs, LambdaIndexerOptions const & options)
     myPrint(options, 1, "Generating Index...");
     double s = sysTime();
 
-    TIndex index{seqs | bio::views::to_rank | fmindex_collection::add_sentinels, 5};
+    TIndex index{seqs | bio::views::to_rank | fmindex_collection::add_sentinels, /*samplingRate*/5, /*threadNbr*/1};
 
     double e = sysTime() - s;
     myPrint(options, 1, " done.\n");

src/search_algo.hpp

@@ -470,11 +470,9 @@ inline void search_impl(LocalDataHolder<TGlobalHolder> & lH, TSeed && seed)
 {
     if constexpr (TGlobalHolder::c_dbIndexType == DbIndexType::FM_INDEX)
     {
-        //!TODO a reversed FMIndex is used, so the query need to be reversed, so we search from left to right
-        //      This is a conceptual TODO for fmindex_collection library
         fmindex_collection::search_backtracking_with_buffers::search(
           lH.gH.indexFile.index,
-          seed | std::views::reverse | bio::views::to_rank | fmindex_collection::add_sentinel,
+          seed | bio::views::to_rank | fmindex_collection::add_sentinel,
           lH.searchOpts.maxSeedDist,
           lH.cursor_tmp_buffer,
           lH.cursor_tmp_buffer2,