Allow disabling derives from references (#57)

* Use postversion instead of postpublish

* Updates

.gitignore

@@ -5,3 +5,4 @@ dist
 *.log
 .vscode/
 esm
+.eslintcache

src/api.ts

@@ -26,6 +26,8 @@ export type {
 
 /** Parser options */
 export interface ParseOptions {
+  /** Whether to resolve references to derives from features */
+  disableDerivesFromReferences?: boolean
   /** Text encoding of the input GFF3. default 'utf8' */
   encoding?: BufferEncoding
   /** Whether to parse features, default true */
@@ -63,6 +65,7 @@ function _processParseOptions(options: ParseOptions): ParseOptionsProcessed {
     parseSequences: true,
     parseComments: false,
     bufferSize: 1000,
+    disableDerivesFromReferences: false,
     ...options,
   }
 
@@ -98,6 +101,7 @@ class GFFTransform extends Transform {
       sequenceCallback: options.parseSequences ? push : undefined,
       errorCallback: (err) => this.emit('error', err),
       bufferSize: options.bufferSize,
+      disableDerivesFromReferences: options.disableDerivesFromReferences,
     })
   }
 
@@ -462,6 +466,7 @@ export function parseStringSync(
     directiveCallback: options.parseDirectives ? push : undefined,
     commentCallback: options.parseComments ? push : undefined,
     sequenceCallback: options.parseSequences ? push : undefined,
+    disableDerivesFromReferences: options.disableDerivesFromReferences || false,
     bufferSize: Infinity,
     errorCallback: (err) => {
       throw err

src/parse.ts

@@ -44,6 +44,7 @@ interface ParserArgs {
   directiveCallback?(directive: GFF3.GFF3Directive): void
   sequenceCallback?(sequence: GFF3.GFF3Sequence): void
   bufferSize?: number
+  disableDerivesFromReferences?: boolean
 }
 
 interface References {
@@ -56,6 +57,7 @@ export default class Parser {
   endCallback: () => void
   commentCallback: (comment: GFF3.GFF3Comment) => void
   errorCallback: (error: string) => void
+  disableDerivesFromReferences: boolean
   directiveCallback: (directive: GFF3.GFF3Directive) => void
   sequenceCallback: (sequence: GFF3.GFF3Sequence) => void
   bufferSize: number
@@ -94,6 +96,8 @@ export default class Parser {
     this.errorCallback = args.errorCallback || nullFunc
     this.directiveCallback = args.directiveCallback || nullFunc
     this.sequenceCallback = args.sequenceCallback || nullFunc
+    this.disableDerivesFromReferences =
+      args.disableDerivesFromReferences || false
 
     // number of lines to buffer
     this.bufferSize = args.bufferSize === undefined ? 1000 : args.bufferSize
@@ -221,7 +225,7 @@ export default class Parser {
     // problem. die with a parse error
     if (Array.from(Object.values(this._underConstructionOrphans)).length) {
       throw new Error(
-        `some features reference other features that do not exist in the file (or in the same '###' scope). ${JSON.stringify(
+        `some features reference other features that do not exist in the file (or in the same '###' scope). ${Object.keys(
           this._underConstructionOrphans,
         )}`,
       )
@@ -241,7 +245,9 @@ export default class Parser {
     // NOTE: a feature is an arrayref of one or more feature lines.
     const ids = featureLine.attributes?.ID || []
     const parents = featureLine.attributes?.Parent || []
-    const derives = featureLine.attributes?.Derives_from || []
+    const derives = this.disableDerivesFromReferences
+      ? []
+      : featureLine.attributes?.Derives_from || []
 
     if (!ids.length && !parents.length && !derives.length) {
       // if it has no IDs and does not refer to anything, we can just

test/data/tair10.gff3

@@ -1,4 +1,4 @@
-1	TAIR10	chromosome      1	30427671	.	.	.	ID=Chr1;Name=Chr1
+1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
 1	TAIR10	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
 1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
 1	TAIR10	protein	3760	5630	.	+	.	ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
@@ -21,4 +21,4 @@
 1	TAIR10	protein	6915	8666	.	-	.	ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
 1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
 1	TAIR10	CDS	8571	8666	.	-	0	Parent=AT1G01020.1,AT1G01020.1-Protein;
-1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1