Fix gff2db segfault, and keep entryname in lookup when multithreaded

src/commons/DBWriter.cpp

@@ -678,7 +678,7 @@ void DBWriter::writeThreadBuffer(unsigned int idx, size_t dataSize) {
     }
 }
 
-void DBWriter::createRenumberedDB(const std::string& dataFile, const std::string& indexFile, const std::string& origData, const std::string& origIndex, int sortMode) {
+void DBWriter::createRenumberedDB(const std::string& dataFile, const std::string& indexFile, const std::string& origData, const std::string& origIndex, bool keepEntryName, int sortMode) {
     DBReader<unsigned int>* lookupReader = NULL;
     FILE *sLookup = NULL;
     if (origData.empty() == false && origIndex.empty() == false) {
@@ -711,7 +711,9 @@ void DBWriter::createRenumberedDB(const std::string& dataFile, const std::string
             size_t lookupId = lookupReader->getLookupIdByKey(idx->id);
             DBReader<unsigned int>::LookupEntry copy = lookup[lookupId];
             copy.id = i;
-            copy.entryName = SSTR(idx->id);
+            if(!keepEntryName){
+                copy.entryName = SSTR(idx->id);
+            }
             lookupReader->lookupEntryToBuffer(strBuffer, copy);
             written = fwrite(strBuffer.c_str(), sizeof(char), strBuffer.size(), sLookup);
             if (written != (int) strBuffer.size()) {

src/commons/DBWriter.h

@@ -59,7 +59,7 @@ class DBWriter : public MemoryTracker  {
     template <typename T>
     static void writeIndexEntryToFile(FILE *outFile, char *buff1, T &index);
 
-    static void createRenumberedDB(const std::string& dataFile, const std::string& indexFile, const std::string& origData, const std::string& origIndex, int sortMode = DBReader<unsigned int>::SORT_BY_ID_OFFSET);
+    static void createRenumberedDB(const std::string& dataFile, const std::string& indexFile, const std::string& origData, const std::string& origIndex, bool keepEntryName = false, int sortMode = DBReader<unsigned int>::SORT_BY_ID_OFFSET);
 
     bool isClosed(){
         return closed;

src/util/convertalignments.cpp

@@ -102,8 +102,9 @@ std::map<unsigned int, unsigned int> readKeyToSet(const std::string& file) {
 
     MemoryMapped lookup(file, MemoryMapped::WholeFile, MemoryMapped::SequentialScan);
     char* data = (char *) lookup.getData();
+    char* end = data + lookup.mappedSize();
     const char* entry[255];
-    while (*data != '\0') {
+    while (data < end && *data != '\0') {
         const size_t columns = Util::getWordsOfLine(data, entry, 255);
         if (columns < 3) {
             Debug(Debug::WARNING) << "Not enough columns in lookup file " << file << "\n";
@@ -125,8 +126,9 @@ std::map<unsigned int, std::string> readSetToSource(const std::string& file) {
 
     MemoryMapped source(file, MemoryMapped::WholeFile, MemoryMapped::SequentialScan);
     char* data = (char *) source.getData();
+    char* end = data + source.mappedSize();
     const char* entry[255];
-    while (*data != '\0') {
+    while (data < end && *data != '\0') {
         const size_t columns = Util::getWordsOfLine(data, entry, 255);
         if (columns < 2) {
             Debug(Debug::WARNING) << "Not enough columns in lookup file " << file << "\n";

src/util/gff2db.cpp

@@ -33,7 +33,7 @@ int gff2db(int argc, const char **argv, const Command &command) {
     headerWriter.open();
     std::string outLookup = outDb + ".lookup";
     std::string outLookupIndex = outDb + ".lookup.index";
-    DBWriter lookupWriter(outLookup.c_str(), outLookupIndex.c_str(), par.threads, 0, Parameters::DBTYPE_OMIT_FILE);
+    DBWriter lookupWriter(outLookup.c_str(), outLookupIndex.c_str(), par.threads, par.compressed, Parameters::DBTYPE_OMIT_FILE);
     lookupWriter.open();
 
     FILE *source = FileUtil::openAndDelete((outDb + ".source").c_str(), "w");
@@ -84,8 +84,9 @@ int gff2db(int argc, const char **argv, const Command &command) {
                 EXIT(EXIT_FAILURE);
             }
             char *data = (char *) file.getData();
+            char* end = data + file.mappedSize();
             size_t idx = 0;
-            while (*data != '\0') {
+            while (data < end && *data != '\0') {
                 // line is a comment or empty
                 if (*data == '#' || *data == '\n') {
                     data = Util::skipLine(data);
@@ -198,7 +199,7 @@ int gff2db(int argc, const char **argv, const Command &command) {
 
 #pragma omp task
                 {
-                    DBWriter::createRenumberedDB(outDb, outDbIndex, outDb, outDbIndex);
+                    DBWriter::createRenumberedDB(outDb, outDbIndex, outDb, outDbIndex, true);
                 }
             }
         }