Add new mask parameters to all modules that mask

Author: milot-mirdita

Diff for: src/commons/Parameters.cpp

@@ -767,7 +767,9 @@ Parameters::Parameters():
     splitsequence.push_back(&PARAM_V);
 
     // mask sequence
+    masksequence.push_back(&PARAM_MASK_RESIDUES);
     masksequence.push_back(&PARAM_MASK_PROBABILTY);
+    masksequence.push_back(&PARAM_MASK_LOWER_CASE);
     masksequence.push_back(&PARAM_MASK_N_REPEAT);
     masksequence.push_back(&PARAM_THREADS);
     masksequence.push_back(&PARAM_COMPRESSED);
@@ -841,6 +843,8 @@ Parameters::Parameters():
     makepaddedseqdb.push_back(&PARAM_SCORE_BIAS);
     makepaddedseqdb.push_back(&PARAM_MASK_RESIDUES);
     makepaddedseqdb.push_back(&PARAM_MASK_PROBABILTY);
+    makepaddedseqdb.push_back(&PARAM_MASK_LOWER_CASE);
+    makepaddedseqdb.push_back(&PARAM_MASK_N_REPEAT);
     makepaddedseqdb.push_back(&PARAM_WRITE_LOOKUP);
     makepaddedseqdb.push_back(&PARAM_THREADS);
     makepaddedseqdb.push_back(&PARAM_V);

Diff for: src/util/masksequence.cpp

@@ -45,7 +45,7 @@ int masksequence(int argc, const char **argv, const Command& command) {
 #pragma omp for schedule(dynamic, 1)
         for (size_t id = 0; id < reader.getSize(); ++id) {
             seq.mapSequence(id, reader.getDbKey(id), reader.getData(id, thread_idx), reader.getSeqLen(id));
-            masker.maskSequence(seq, true, par.maskProb, par.maskLowerCaseMode, par.maskNrepeats);
+            masker.maskSequence(seq, par.mask, par.maskProb, par.maskLowerCaseMode, par.maskNrepeats);
             memcpy(charSequence, seq.getSeqData(), seq.L * sizeof(char));
             masker.applySoftmasking(charSequence, seq.numSequence, seq.L);
             charSequence[seq.L] = '\n';