ca3m segfault same db

soedinglab · Jun 29, 2023 · f5f780a · f5f780a
1 parent 2568829
commit f5f780a
Showing 1 changed file with 4 additions and 6 deletions.
diff --git a/src/util/result2msa.cpp b/src/util/result2msa.cpp
@@ -36,6 +36,7 @@ int result2msa(int argc, const char **argv, const Command &command) {
     IndexReader *tDbrIdx = NULL;
     DBReader<unsigned int> *targetHeaderReader = NULL;
     IndexReader *targetHeaderReaderIdx = NULL;
+    const bool sameDatabase = (par.db1.compare(par.db2) == 0) ? true : false;
 
     if (Parameters::isEqualDbtype(FileUtil::parseDbType(par.db2.c_str()), Parameters::DBTYPE_INDEX_DB)) {
         if (isCA3M == true) {
@@ -58,7 +59,7 @@ int result2msa(int argc, const char **argv, const Command &command) {
         if (par.preloadMode != Parameters::PRELOAD_MODE_MMAP) {
             tDbr->readMmapedDataInMemory();
         }
-        if (isCA3M == false) {
+        if (isCA3M == false || sameDatabase) {
             targetHeaderReader = new DBReader<unsigned int>(par.hdr2.c_str(), par.hdr2Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX | DBReader<unsigned int>::USE_DATA);
             targetHeaderReader->open(DBReader<unsigned int>::NOSORT);
             if (par.preloadMode != Parameters::PRELOAD_MODE_MMAP) {
@@ -69,7 +70,6 @@ int result2msa(int argc, const char **argv, const Command &command) {
 
     DBReader<unsigned int> *qDbr = NULL;
     DBReader<unsigned int> *queryHeaderReader = NULL;
-    const bool sameDatabase = (par.db1.compare(par.db2) == 0) ? true : false;
     if (!sameDatabase) {
         qDbr = new DBReader<unsigned int>(par.db1.c_str(), par.db1Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX | DBReader<unsigned int>::USE_DATA);
         qDbr->open(DBReader<unsigned int>::NOSORT);
@@ -209,15 +209,13 @@ int result2msa(int argc, const char **argv, const Command &command) {
 #pragma omp for schedule(dynamic, 10)
         for (size_t id = dbFrom; id < (dbFrom + dbSize); id++) {
             progress.updateProgress();
-
             unsigned int queryKey = resultReader.getDbKey(id);
             size_t queryId = qDbr->getId(queryKey);
             if (queryId == UINT_MAX) {
                 Debug(Debug::WARNING) << "Invalid query sequence " << queryKey << "\n";
                 continue;
             }
             centerSequence.mapSequence(queryId, queryKey, qDbr->getData(queryId, thread_idx), qDbr->getSeqLen(queryId));
-
             // TODO: Do we still need this?
 //            if (centerSequence.L) {
 //                // remove last in it is a *
@@ -231,18 +229,19 @@ int result2msa(int argc, const char **argv, const Command &command) {
                 Debug(Debug::WARNING) << "Invalid query header " << queryKey << "\n";
                 continue;
             }
+
             char *centerSequenceHeader = queryHeaderReader->getData(centerHeaderId, thread_idx);
             size_t centerHeaderLength = queryHeaderReader->getEntryLen(centerHeaderId) - 1;
 
             if (par.msaFormatMode == Parameters::FORMAT_MSA_STOCKHOLM_FLAT) {
                 accession = Util::parseFastaHeader(centerSequenceHeader);
             }
 
-
             bool isQueryInit = false;
             char *data = resultReader.getData(id, thread_idx);
             while (*data != '\0') {
                 Util::parseKey(data, dbKey);
+
                 const unsigned int key = (unsigned int) strtoul(dbKey, NULL, 10);
                 // in the same database case, we have the query repeated
                 if (key == queryKey && sameDatabase == true) {
@@ -520,7 +519,6 @@ int result2msa(int argc, const char **argv, const Command &command) {
                     }
                     result.append("\n;");
                 }
-
                 Matcher::result_t queryAln;
                 unsigned int newQueryKey = seqConcat->dbAKeyMap(queryKey);
                 queryAln.qStartPos = 0;