Fix new index-subset 8/10

Author: milot-mirdita

src/commons/Parameters.cpp

@@ -198,7 +198,7 @@ Parameters::Parameters():
         // indexdb
         PARAM_CHECK_COMPATIBLE(PARAM_CHECK_COMPATIBLE_ID, "--check-compatible", "Check compatible", "0: Always recreate index, 1: Check if recreating index is needed, 2: Fail if index is incompatible", typeid(int), (void *) &checkCompatible, "^[0-2]{1}$", MMseqsParameter::COMMAND_MISC),
         PARAM_SEARCH_TYPE(PARAM_SEARCH_TYPE_ID, "--search-type", "Search type", "Search type 0: auto 1: amino acid, 2: translated, 3: nucleotide, 4: translated nucleotide alignment", typeid(int), (void *) &searchType, "^[0-4]{1}"),
-        PARAM_INDEX_SUBSET(PARAM_INDEX_SUBSET_ID, "--index-subset", "Index subset", "Create specialized index with subset of entries\n0: normal index\n1: index without headers\n2: index without prefiltering data\n4: index without aln (for cluster db)\n8: no sequence lookup (good for GPU only searches)\nFlags can be combined bit wise", typeid(int), (void *) &indexSubset, "^[0-7]{1}", MMseqsParameter::COMMAND_EXPERT),
+        PARAM_INDEX_SUBSET(PARAM_INDEX_SUBSET_ID, "--index-subset", "Index subset", "Create specialized index with subset of entries\n0: normal index\n1: index without headers\n2: index without prefiltering data\n4: index without aln (for cluster db)\n8: no sequence lookup (good for GPU only searches)\nFlags can be combined bit wise", typeid(int), (void *) &indexSubset, "^[0-9]{1}[0-9]*$", MMseqsParameter::COMMAND_EXPERT),
         PARAM_INDEX_DBSUFFIX(PARAM_INDEX_DBSUFFIX_ID, "--index-dbsuffix", "Index dbsuffix", "A suffix of the db (used for cluster dbs)", typeid(std::string), (void *) &indexDbsuffix, "", MMseqsParameter::COMMAND_HIDDEN),
         // createdb
         PARAM_USE_HEADER(PARAM_USE_HEADER_ID, "--use-fasta-header", "Use fasta header", "Use the id parsed from the fasta header as the index key instead of using incrementing numeric identifiers", typeid(bool), (void *) &useHeader, ""),

src/prefiltering/PrefilteringIndexReader.cpp

@@ -236,10 +236,10 @@ void PrefilteringIndexReader::createIndexFile(const std::string &outDB,
             IndexBuilder::fillDatabase(indexTable, &sequenceLookup,
                                        *subMat, s3, s2, &seq, dbr1, dbFrom, dbFrom + dbSize, kmerThr,
                                        maskMode, maskLowerCase, maskProb, maskNrepeats, targetSearchMode);
-        }
-        if (sequenceLookup == NULL) {
-            Debug(Debug::ERROR) << "Invalid mask mode. No sequence lookup created!\n";
-            EXIT(EXIT_FAILURE);
+            if (sequenceLookup == NULL) {
+                Debug(Debug::ERROR) << "Invalid mask mode. No sequence lookup created!\n";
+                EXIT(EXIT_FAILURE);
+            }
         }
         unsigned int keyOffset = 1000 * s;
         if(needKmerIndex){
@@ -267,14 +267,15 @@ void PrefilteringIndexReader::createIndexFile(const std::string &outDB,
             writer.alignToPageSize(SPLIT_INDX + s);
 
         }
-        // SEQCOUNT
-        Debug(Debug::INFO) << "Write SEQCOUNT (" << (keyOffset + SEQCOUNT) << ")\n";
-        size_t tablesize = sequenceLookup->getSequenceCount();
-        char *tablesizePtr = (char *) &tablesize;
-        writer.writeData(tablesizePtr, 1 * sizeof(size_t), (keyOffset + SEQCOUNT), SPLIT_INDX + s);
-        writer.alignToPageSize(SPLIT_INDX + s);
-
-        if(needSequenceLookup){
+
+        if (needSequenceLookup) {
+            // SEQCOUNT
+            Debug(Debug::INFO) << "Write SEQCOUNT (" << (keyOffset + SEQCOUNT) << ")\n";
+            size_t tablesize = sequenceLookup->getSequenceCount();
+            char *tablesizePtr = (char *) &tablesize;
+            writer.writeData(tablesizePtr, 1 * sizeof(size_t), (keyOffset + SEQCOUNT), SPLIT_INDX + s);
+            writer.alignToPageSize(SPLIT_INDX + s);
+
             Debug(Debug::INFO) << "Write SEQINDEXDATASIZE (" << (keyOffset + SEQINDEXDATASIZE) << ")\n";
             int64_t seqindexDataSize = sequenceLookup->getDataSize();
             char *seqindexDataSizePtr = (char *) &seqindexDataSize;
@@ -288,8 +289,9 @@ void PrefilteringIndexReader::createIndexFile(const std::string &outDB,
             Debug(Debug::INFO) << "Write SEQINDEXDATA (" << (keyOffset + SEQINDEXDATA) << ")\n";
             writer.writeData(sequenceLookup->getData(), (sequenceLookup->getDataSize() + 1) * sizeof(char), (keyOffset + SEQINDEXDATA), SPLIT_INDX + s);
             writer.alignToPageSize(SPLIT_INDX + s);
+
+            delete sequenceLookup;
         }
-        delete sequenceLookup;
         if(indexTable != NULL){
             delete indexTable;
         }