always run postannotation and set ID even if error in annotation

brentp · Mar 18, 2017 · 2ac41a1 · 2ac41a1
1 parent 5f96ad2
commit 2ac41a1
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Showing 4 changed files with 11 additions and 7 deletions.
diff --git a/api/api.go b/api/api.go
@@ -716,13 +716,13 @@ func (a *Annotator) AnnotateEnds(v interfaces.Relatable, ends string) error {
 	}
 	if ends == INTERVAL {
 		err := a.AnnotateOne(v, a.Strict)
-		if err != nil {
-			return err
-		}
 		err2, newid := a.PostAnnotate(v.Chrom(), int(v.Start()), int(v.End()), v.(interfaces.IVariant).Info(), "", id)
 		if newid != "" {
 			v.(*parsers.Variant).IVariant.(*vcfgo.Variant).Id_ = newid
 		}
+		if err != nil {
+			return err
+		}
 		return err2
 	}
 	// hack:

diff --git a/docs/CHANGES.md b/docs/CHANGES.md
@@ -1,3 +1,7 @@
+v0.2.2
+------
++ wholely fix order of error checking from postannotation (affects users using ID annotation) (thanks @vladsaveliev)
+
 v0.2.1
 ------
 + correct order of error-checking on return from postannotation (affects users using ID annotation)

diff --git a/tests/id-test/small.toml b/tests/id-test/small.toml
@@ -1,8 +1,8 @@
 [[annotation]]
 file="tests/id-test/dbsnp.small.vcf.gz"
-fields=["ID"]
-names=["rs_ids"]
-ops=["self"] 
+fields=["ID", "CAF"]
+names=["rs_ids", "CAF"]
+ops=["self", "self"]
 
 [[annotation]]
 file="tests/id-test/cosmic.small.vcf.gz"

diff --git a/vcfanno.go b/vcfanno.go
@@ -24,7 +24,7 @@ import (
 	"github.com/brentp/xopen"
 )
 
-var VERSION = "0.2.1"
+var VERSION = "0.2.2"
 
 func envGet(name string, vdefault int) int {
 	sval := os.Getenv(name)