create-taxdump: fix circular definition in merged.dmp. shenwei356/gtd…

…b-taxdump#2
shenwei356 · Aug 25, 2022 · cc261ad · cc261ad
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,7 +2,7 @@
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.12.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.1)
     - `taxonkit reformat`: add a new placeholder `{K}` for rank `kingdom`. [#64](https://github.com/shenwei356/taxonkit/issues/64)
     - `taxonkit create-taxdump`: 
-        - fix merged.dmp and delnodes.dmp. [gtdb-taxdump/issues/2](https://github.com/shenwei356/gtdb-taxdump/issues/2)
+        - fix merged.dmp and delnodes.dmp. Thanks to @apcamargo ! [gtdb-taxdump/issues/2](https://github.com/shenwei356/gtdb-taxdump/issues/2).
         - fix bug of handling non-GTDB data when using `-A/--field-accession` and no rank names given.
     - `taxonkit reformat`: do not panic for invalid TaxIds, e.g., the column name, when using `-I--taxid-field`.
 - [TaxonKit v0.12.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)

diff --git a/taxonkit/cmd/create-taxdump.go b/taxonkit/cmd/create-taxdump.go
@@ -778,6 +778,13 @@ Attentions:
 
 			// append old merged.dmp
 			for from, to := range taxdb.MergeNodes {
+				// https://github.com/shenwei356/gtdb-taxdump/issues/2#issuecomment-1226186877
+				// The history of GCF_001405015.1 showed Clostridium disporicum was renamed to
+				// Clostridium disporicum_A in R95, and changed back in R207.
+				if _, ok = merged[to]; ok && merged[to] == from {
+					// delnodes[to] = struct{}{}
+					continue
+				}
 				if _, ok = delnodes[to]; ok { // could not append deleted nodes
 					delnodes[from] = struct{}{} // if the new taxid has been deleted, mark the old taxid too
 					continue