From 2cd1fded1034c2a6e133f4bd30fc453f24d19e1b Mon Sep 17 00:00:00 2001
From: Aleksey Zimin <alekseyz@salz4.idies.jhu.edu>
Date: Tue, 21 Jun 2022 16:47:14 -0400
Subject: [PATCH] better performance in build and fix for --work-on-disk option

---
 scripts/build_db.sh |  2 +-
 src/set_lcas.cpp    | 16 +++++++++-------
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/scripts/build_db.sh b/scripts/build_db.sh
index 603a83a..0641fd1 100755
--- a/scripts/build_db.sh
+++ b/scripts/build_db.sh
@@ -235,7 +235,7 @@ else
     exe eval tar zxf taxdump.tar.gz
     cd ..
   fi
-  build_taxdb $TAXONOMY_DIR/names.dmp $TAXONOMY_DIR/nodes.dmp | sort -t$'\t' -rnk6,6 -rnk5,5 > taxDB.tmp
+  build_taxdb $TAXONOMY_DIR/names.dmp $TAXONOMY_DIR/nodes.dmp | sort -S 20% -t$'\t' -rnk6,6 -rnk5,5 > taxDB.tmp
   mv taxDB.tmp taxDB
   echo "taxDB construction finished. [$(report_time_elapsed $start_time1)]"
 fi
diff --git a/src/set_lcas.cpp b/src/set_lcas.cpp
index 2a15e7d..b944f28 100644
--- a/src/set_lcas.cpp
+++ b/src/set_lcas.cpp
@@ -113,10 +113,10 @@ int main(int argc, char **argv) {
     }
   }
 
-  if (!Operate_in_RAM && Output_DB_filename.size() > 0) {
-      cerr << "You need to operate in RAM (flag -M) to use output to a different file (flag -o)" << endl;
-      return 1;
-  }
+  //if (!Operate_in_RAM && Output_DB_filename.size() > 0) {
+  //    cerr << "You need to operate in RAM (flag -M) to use output to a different file (flag -o)" << endl;
+  //    return 1;
+  //}
 
   QuickFile db_file(DB_filename, "rw");
   size_t db_file_size = db_file.size();
@@ -126,9 +126,6 @@ int main(int argc, char **argv) {
     dat = slurp_file(DB_filename, db_file_size);
     Database = KrakenDB(dat.data());
   } else {
-    if (Output_DB_filename.size() > 0) {
-      //system("cp " + DB_filename + " " + Output_DB_filename);
-    }
     Database = KrakenDB(db_file.ptr());
   }
 
@@ -162,6 +159,11 @@ int main(int argc, char **argv) {
     ofs.write(dat.data(), db_file_size);
     ofs.close();
     dat.clear();
+  } else if (!Pretend) {
+    if (Output_DB_filename.size() > 0) {
+      string cmd="cp " + DB_filename + " " + Output_DB_filename;
+      system(cmd.c_str());
+    }
   }
 
   UID_map_file.close();