handle missing value in postannotation. closes #116

brentp · Apr 15, 2020 · 9f857a9 · 9f857a9
1 parent 1d140d4
commit 9f857a9
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Showing 5 changed files with 20 additions and 1 deletion.
diff --git a/api/api.go b/api/api.go
@@ -638,7 +638,7 @@ func (a *Annotator) PostAnnotate(chrom string, start int, end int, info interfac
 				}
 			}
 			// we need to try even if it didn't get all values.
-			if len(vals) == 0 && len(post.Fields) > 0 {
+			if len(vals) == 0 && len(post.Fields) == 0 {
 				continue
 			}
 

diff --git a/tests/functional-test.sh b/tests/functional-test.sh
@@ -194,3 +194,8 @@ assert_exit_code 0
 assert_equal $(tail -1 $STDOUT_FILE | cut -f 8) "AF=1.56250e-02;AQ=1328;CADD_RAW=0.591814"
 go install -a
 
+
+run check_missing_postanno vcfanno -lua tests/missing_postanno/o.lua tests/missing_postanno/o.conf tests/missing_postanno/o.vcf
+assert_exit_code 0
+assert_in_stdout "exome_af=-1"
+
diff --git a/tests/missing_postanno/o.conf b/tests/missing_postanno/o.conf
@@ -0,0 +1,5 @@
+[[postannotation]]
+fields=["exome_af"]
+op="lua:checkaf(exome_af)"
+name="exome_af"
+type="Float"
diff --git a/tests/missing_postanno/o.lua b/tests/missing_postanno/o.lua
@@ -0,0 +1,5 @@
+function checkaf(v)
+  local output = v
+  if (v == nil) then output = -1 end
+  return output
+end
diff --git a/tests/missing_postanno/o.vcf b/tests/missing_postanno/o.vcf
@@ -0,0 +1,4 @@
+##fileformat=VCFv4.1
+##INFO=<ID=exome_af,Number=1,Type=Float,Description="xxx">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr1	123456	.	G	T	.	PASS	.