Warn users if one of the input files is empty or invalid

soedinglab · Apr 11, 2023 · 10e0f1b · 10e0f1b
1 parent 3626bdb
commit 10e0f1b
Showing 1 changed file with 8 additions and 3 deletions.
diff --git a/src/util/createdb.cpp b/src/util/createdb.cpp
@@ -184,7 +184,7 @@ int createdb(int argc, const char **argv, const Command& command) {
             progress.updateProgress();
             const KSeqWrapper::KSeqEntry &e = kseq->entry;
             if (e.name.l == 0) {
-                Debug(Debug::ERROR) << "Fasta entry " << entries_num << " is invalid\n";
+                Debug(Debug::ERROR) << "Fasta entry " << numEntriesInCurrFile << " is invalid\n";
                 EXIT(EXIT_FAILURE);
             }
 
@@ -199,7 +199,7 @@ int createdb(int argc, const char **argv, const Command& command) {
                 std::string headerId = Util::parseFastaHeader(header.c_str());
                 if (headerId.empty()) {
                     // An identifier is necessary for these two cases, so we should just give up
-                    Debug(Debug::WARNING) << "Cannot extract identifier from entry " << entries_num << "\n";
+                    Debug(Debug::WARNING) << "Cannot extract identifier from entry " << numEntriesInCurrFile << "\n";
                 }
                 header.push_back('\n');
             }
@@ -233,7 +233,7 @@ int createdb(int argc, const char **argv, const Command& command) {
             if (par.createdbMode == Parameters::SEQUENCE_SPLIT_MODE_SOFT) {
                 if (e.newlineCount != 1) {
                     if (e.newlineCount == 0) {
-                        Debug(Debug::WARNING) << "Fasta entry " << entries_num << " has no newline character\n";
+                        Debug(Debug::WARNING) << "Fasta entry " << numEntriesInCurrFile << " has no newline character\n";
                     } else if (e.newlineCount > 1) {
                         Debug(Debug::WARNING) << "Multiline fasta can not be combined with --createdb-mode 0\n";
                     }
@@ -273,6 +273,11 @@ int createdb(int argc, const char **argv, const Command& command) {
             numEntriesInCurrFile++;
             header.clear();
         }
+
+        if (numEntriesInCurrFile == 0) {
+            Debug(Debug::WARNING) << "File " << sourceName << " is empty or invalid and was ignored\n";
+        }
+
         delete kseq;
         if (filenames.size() > 1 && par.createdbMode == Parameters::SEQUENCE_SPLIT_MODE_SOFT) {
             size_t fileSize = FileUtil::getFileSize(filenames[fileIdx].c_str());