Fixed merge conflicts

CHANGELOG.md

@@ -4,6 +4,7 @@ All notable changes to Pantools will be documented in this file.
 
 ### Added
 - Added check to `add_variants` to ensure that the input VCF file contains sequences that occur in the pangenome (!263).
+- Added check to `optimal_grouping` to ensure that the required BUSCO directory exists before running (!269).
 - Added additional command-line parameter `minimum-fraction-threshold` to `msa` to modify trimming of sequences (!267).
 
 ## [4.3.3] - 21-02-2025

src/main/java/nl/wur/bif/pantools/construction/grouping/Grouping.java

@@ -1057,7 +1057,18 @@ public class Grouping {
         if (Mode.contains("FAST")) {
             FAST = true; // check if the F1 score dropped compared to the previous grouping, stop when this is the case
         }
-        Pantools.logger.info("Finding the most optimal setting for 'group'.");
+        Pantools.logger.info("Finding the most optimal setting for 'group' using BUSCO results.");
+
+        // check that BUSCO has been run
+        try (Transaction tx = GRAPH_DB.beginTx()) { // start database transaction
+            skip.create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
+            update_skip_array_based_on_anno_ids();
+            tx.success(); // transaction successful, commit changes
+        } catch (NotFoundException nfe) {
+            Pantools.logger.error("Unable to start the database.");
+            System.exit(1);
+        }
+        findBuscoInputDirectory();
 
         // check for heap space (8g multiplied by .8 because only ~85% of the Xmx setting is usually available.)
         if (Runtime.getRuntime().maxMemory() < 8589934592L * .8) {
@@ -2292,7 +2303,7 @@ public class Grouping {
                     String error_string = foundPhasedBuscoOutput.toString().replace(",", "\n ").replace("[", "").replace("]", "");
                     Pantools.logger.error(error_string);
                 }
-                System.exit(1);
+                throw new RuntimeException("BUSCO input files not found");
             }
         }
         return buscoDirectory.replace("//","/"); // the path is later split on /