🔧 description testing updates

Author: dmiller15

src/commands/encoder_cmd.rs

@@ -241,7 +241,7 @@ pub fn encoder_main(vpaths: Vec<&str>, opath: &str, jpath: &str) {
             TagLength::Genotypes => f.number = "G".to_string(),
             TagLength::Variable => f.number = ".".to_string(),
         };
-        if f.description == fields::default_description_string() {
+        if f.field != "FILTER" && f.description == fields::default_description_string() {
             f.description = hdr_info_id2description(header.header_records(), &f.field, &f.description);
         };
     }

tests/big.sh

@@ -23,15 +23,17 @@ for mod in 2 3 4 5; do
 
 
         if [[ "mod" -ne "1" ]]; then
-            # now annotate with both and all values shouldl be annotated.
-            echo "two echtvars check"
-	    $echtvar encode test.echtvar1 test1.hjson generated-subset1.vcf
-	    $echtvar anno generated-all.vcf -e test.echtvar0 -e test.echtvar1 anno.vcf.gz
-  	    python3 check.py anno.vcf.gz 1
-		# check default Description used
-		python3 check-string-for-issue33.py anno.vcf.gz aval1 1 "added by echtvar from test.echtvar1"
-		# check value . is left alone
-		python3 check-string-for-issue33.py anno.vcf.gz external_str . "added by echtvar from test.echtvar1"
+                # now annotate with both and all values should be annotated.
+                echo "two echtvars check"
+                $echtvar encode test.echtvar1 test1.hjson generated-subset1.vcf
+                $echtvar anno generated-all.vcf -e test.echtvar0 -e test.echtvar1 anno.vcf.gz
+                python3 check.py anno.vcf.gz 1
+                # check that the default Description is used when no JSON value or encode Description
+                python3 check-string-for-issue33.py anno.vcf.gz no_description 1 "added by echtvar from test.echtvar1"
+                # check that the encode Description is used when no JSON value
+                python3 check-string-for-issue33.py anno.vcf.gz aval1 1 "added by echtvar random value"
+                # check value . is left alone
+                python3 check-string-for-issue33.py anno.vcf.gz external_str . "added by echtvar string value"
         fi
 
 

tests/make-vcf.py

@@ -15,6 +15,7 @@
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate allele count">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles">
 ##INFO=<ID=val%s,Number=1,Type=Integer,Description="random value">
+##INFO=<ID=nodesc,Number=1,Type=Integer>
 ##INFO=<ID=nvar,Number=1,Type=Integer,Description="variant index">
 ##INFO=<ID=str,Number=.,Type=String,Description="string value">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate allele frequency">

tests/test1.hjson

@@ -1,4 +1,5 @@
 [
   {"field": "val1", "alias": "aval1"},
-  {"field": "str", "alias": "external_str"}
+  {"field": "str", "alias": "external_str"},
+  {"field": "nodesc", "alias": "no_description"}
 ]