Fix keeping taxids with a rank of "no rank" or "clade". #97

shenwei356 · Apr 25, 2024 · 668d610 · 668d610
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,7 @@
+- [TaxonKit v0.16.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.1)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.1)
+    - `taxonkit filter`:
+        - Fix keeping taxids with a rank of "no rank" or "clade". [#97](https://github.com/shenwei356/taxonkit/issues/97)
 - [TaxonKit v0.16.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
     - `taxonkit create-taxdump`:

diff --git a/taxonkit/cmd/util-filter.go b/taxonkit/cmd/util-filter.go
@@ -223,6 +223,9 @@ func (f *rankFilter) isPassed(taxid uint32) (bool, error) {
 				f.cache[taxid] = false
 				return false, nil
 			}
+		} else { // all nonrank will be outputted if !discardNorank
+			f.cache[taxid] = true
+			return true, nil
 		}
 	}
 
@@ -267,7 +270,7 @@ func (f *rankFilter) isPassed(taxid uint32) (bool, error) {
 		}
 	}
 
-	order, _ := f.rankOrder[rank]
+	order := f.rankOrder[rank]
 	// order, ok := f.rankOrder[rank]
 	// if !ok {
 	// 	return false, fmt.Errorf("rank order not defined in rank file: %s", rank)