Merge commit '0404da93c107839b45f2bc4578df5dcd72cc3d70'

steineggerlab · Jan 13, 2025 · fe4a89a · fe4a89a
2 parents 68388e2 + 0404da9
commit fe4a89a
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Showing 3 changed files with 8 additions and 1 deletion.
diff --git a/lib/mmseqs/src/commons/Parameters.cpp b/lib/mmseqs/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 --git a/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp b/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp
@@ -289,6 +289,9 @@ void PrefilteringIndexReader::createIndexFile(const std::string &outDB,
         writer.writeData(sequenceLookup->getData(), (sequenceLookup->getDataSize() + 1) * sizeof(char), (keyOffset + SEQINDEXDATA), SPLIT_INDX + s);
         writer.alignToPageSize(SPLIT_INDX + s);
         delete sequenceLookup;
+        if(indexTable != NULL){
+            delete indexTable;
+        }
     }
 
     if (Parameters::isEqualDbtype(seqType, Parameters::DBTYPE_HMM_PROFILE) == false && indexSubset != Parameters::INDEX_SUBSET_NO_PREFILTER) {

diff --git a/lib/mmseqs/src/util/masksequence.cpp b/lib/mmseqs/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.maskMode, 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';