Merge pull request #21 from mourisl/gtdb

Fix an issue of creating redundant intermediate nodes in the taxonomy tree
mourisl · Nov 20, 2024 · 05283f0 · 05283f0
2 parents dc25bd3 + 985f94d
commit 05283f0
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/defs.h b/defs.h
@@ -5,7 +5,7 @@
 
 //#define DEBUG
 
-#define CENTRIFUGER_VERSION "1.0.6-r175"
+#define CENTRIFUGER_VERSION "1.0.6-r178"
 
 extern char nucToNum[26] ; 
 extern char numToNuc[26] ;

diff --git a/indices/gtdb-create-dmp.pl b/indices/gtdb-create-dmp.pl
@@ -169,12 +169,18 @@ sub system_call
     else
     {
       $ltid = $novelTaxId ;
-      $ncbiNamesToTaxId{$lineageFields[$j]} = $ltid ;
+      #$ncbiNamesToTaxId{$lineageFields[$j]} = $ltid ;
+      $newNamesToTaxId{$lineageFields[$j]} = $ltid ; 
       ++$novelTaxId ;
     }
 
     $taxid = $ltid if ($j == scalar(@lineageFields) - 1) ;
 
+    if (defined $nodesToPrint{$ltid} && $nodesToPrint{$ltid} != $parentTid)
+    {
+      die "A conflict of lineage information is found when processing $lineage\n" ;
+    }
+
     $nodesToPrint{$ltid} = $parentTid ;
     $taxIdRank{$ltid} = $cols2[0] ;
     $namesToPrint{$ltid} = $cols2[1]  ;