Merge branch 'master' of https://github.com/soedinglab/mmseqs2

Author: martin-steinegger

.travis.yml

@@ -21,7 +21,7 @@ jobs:
         - g++-8
         - gcc-8
     arch: arm64
-    env: CC=gcc-8 CXX=g++-8 MMSEQS_NUM_THREADS=8
+    env: CC=gcc-8 CXX=g++-8 MMSEQS_NUM_THREADS=4
     dist: bionic
   - addons:
       apt:

src/commons/Parameters.cpp

@@ -1201,14 +1201,10 @@ Parameters::Parameters():
     taxonomy.push_back(&PARAM_ORF_FILTER_S);
     taxonomy.push_back(&PARAM_LCA_MODE);
     taxonomy.push_back(&PARAM_TAX_OUTPUT_MODE);
+    taxonomy = combineList(taxonomy, aggregatetaxweights);
     taxonomy = combineList(taxonomy, lca);
     taxonomy = combineList(taxonomy, searchworkflow);
 
-    // taxpercontig
-    taxpercontig = combineList(taxonomy, aggregatetax);
-    removeParameter(taxpercontig, PARAM_TRANSLATE);
-    removeParameter(taxpercontig, PARAM_TAX_OUTPUT_MODE);
-
     // easy taxonomy
     easytaxonomy = combineList(taxonomy, addtaxonomy);
     easytaxonomy = combineList(easytaxonomy, taxonomyreport);

src/commons/Parameters.h

@@ -1066,7 +1066,6 @@ class Parameters {
     std::vector<MMseqsParameter*> aggregatetax;
     std::vector<MMseqsParameter*> aggregatetaxweights;
     std::vector<MMseqsParameter*> taxonomy;
-    std::vector<MMseqsParameter*> taxpercontig;
     std::vector<MMseqsParameter*> easytaxonomy;
     std::vector<MMseqsParameter*> createsubdb;
     std::vector<MMseqsParameter*> renamedbkeys;