Merge pull request #58 from jaebeom-kim/master

Record the Metabuli commit used for database creation
steineggerlab · Mar 20, 2024 · 4305aa5 · 4305aa5
2 parents 77ea100 + 6eeb7e5
commit 4305aa5
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Showing 3 changed files with 9 additions and 1 deletion.
diff --git a/src/commons/IndexCreator.cpp b/src/commons/IndexCreator.cpp
@@ -9,6 +9,8 @@
 #include "NcbiTaxonomy.cpp"
 #include "common.h"
 
+extern const char *version;
+
 IndexCreator::IndexCreator(const LocalParameters & par) {
  // Parameters
  threadNum = par.threads;
@@ -1050,6 +1052,7 @@ void IndexCreator::writeDbParameters() {
  }
  fprintf(handle, "DB_name\t%s\n", dbName.c_str());
  fprintf(handle, "Creation_date\t%s\n", dbDate.c_str());
+ fprintf(handle, "Metabuli commit used to create the DB\t%s\n", version);
  fprintf(handle, "Reduced_alphabet\t%d\n", reducedAA);
  fprintf(handle, "Spaced_kmer_mask\t%s\n", spaceMask.c_str());
  fprintf(handle, "Accession_level\t%d\n", accessionLevel);

diff --git a/src/commons/LocalParameters.cpp b/src/commons/LocalParameters.cpp
@@ -7,6 +7,8 @@
 #include <iomanip>
 #include "DistanceCalculator.h"
 
+extern const char *version;
+
 LocalParameters::LocalParameters() :
  Parameters(),
  VIRUS_TAX_ID(VIRUS_TAX_ID_ID,
@@ -419,7 +421,7 @@ void LocalParameters::printParameters(const std::string &module, int argc, const
  std::stringstream ss;
  ss << std::boolalpha;
 
-  ss << std::setw(maxWidth) << std::left << "Metabuli Version:" << "\t" << "1.0.2" << "\n";
+ ss << std::setw(maxWidth) << std::left << "Metabuli Version (commit):" << "\t" << version << "\n";
 
  for (size_t i = 0; i < par.size(); i++) {
  if (par[i]->category & MMseqsParameter::COMMAND_HIDDEN) {

diff --git a/src/workflow/add_to_library.cpp b/src/workflow/add_to_library.cpp
@@ -28,11 +28,14 @@ int addToLibrary(int argc, const char **argv, const Command &command){
  if (par.taxonomyPath == "DBDIR/taxonomy/") par.taxonomyPath = dbDir + "/taxonomy/";
  if (par.libraryPath == "DBDIR/library/") par.libraryPath = dbDir + "/library/";
 
+
+
  // If the library directory does not exist, create it
  if (!FileUtil::directoryExists(par.libraryPath.c_str())) {
  FileUtil::makeDir(par.libraryPath.c_str());
  }
 
+
  // Load taxonomy
  NcbiTaxonomy * taxonomy = loadTaxonomy(dbDir, par.taxonomyPath);