feat: set the default sequence when there is only a single sequence i…

…n the reference genomes closes #454
GenSpectrum · Jul 18, 2024 · 0ae4022 · 0ae4022
1 parent 287bb8b
commit 0ae4022
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/include/silo/preprocessing/preprocessor.h b/include/silo/preprocessing/preprocessor.h
@@ -43,6 +43,7 @@ class Preprocessor {
    Database preprocess();
 
   private:
+   void finalizeConfig();
    void validateConfig();
 
    static std::string makeNonNullKey(const std::string& field);

diff --git a/src/silo/preprocessing/preprocessor.cpp b/src/silo/preprocessing/preprocessor.cpp
@@ -63,7 +63,7 @@ Preprocessor::Preprocessor(
 }
 
 Database Preprocessor::preprocess() {
-   validateConfig();
+   finalizeConfig();
 
    SPDLOG_INFO(
       "preprocessing - creating intermediate results directory '{}'",
@@ -128,6 +128,17 @@ Database Preprocessor::preprocess() {
    );
 }
 
+void Preprocessor::finalizeConfig() {
+   if (nuc_sequences.size() == 1 && !database_config.default_nucleotide_sequence.has_value()) {
+      database_config.default_nucleotide_sequence = nuc_sequences.at(0);
+   }
+   if (aa_sequences.size() == 1 && !database_config.default_amino_acid_sequence.has_value()) {
+      database_config.default_amino_acid_sequence = aa_sequences.at(0);
+   }
+
+   validateConfig();
+}
+
 void Preprocessor::validateConfig() {
    const bool default_nucleotide_sequence_is_not_in_reference =
       database_config.default_nucleotide_sequence.has_value() &&