fix: correct multi-location feature handling in parseRecordsJBrowse, misc cleanup

- Fix bug where duplicate IDs in JBrowse parsing would still process parent
  relationships on the discarded feature, creating dangling subfeature refs
- Reorder FASTA/> break checks before comment skip in stringToRecords
- Simplify parseDirective to use direct index access instead of two destructures
- Remove dead _lineHash skip in parseAttributesJBrowseImpl
- Use trimEnd

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: cmdcolin

src/api.ts

@@ -44,15 +44,12 @@ function stringToRecords(str: string) {
   const lines = str.split(/\r?\n/)
   const records: LineRecord[] = []
   for (const line of lines) {
+    if (line.startsWith('##FASTA') || line.startsWith('>')) {
+      break
+    }
     if (line.length === 0 || line.startsWith('#')) {
-      if (line.startsWith('##FASTA')) {
-        break
-      }
       continue
     }
-    if (line.startsWith('>')) {
-      break
-    }
     records.push({
       line,
       start: 0,
@@ -174,20 +171,21 @@ export function parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[] {
       continue
     }
 
+    if (id && byId.has(id)) {
+      continue
+    }
+
     if (id) {
-      const existing = byId.get(id)
-      if (!existing) {
-        if (!parent) {
-          items.push(feature)
-        }
-        byId.set(id, feature)
-        const waiting = orphans.get(id)
-        if (waiting) {
-          for (const w of waiting) {
-            feature.subfeatures.push(w)
-          }
-          orphans.delete(id)
+      if (!parent) {
+        items.push(feature)
+      }
+      byId.set(id, feature)
+      const waiting = orphans.get(id)
+      if (waiting) {
+        for (const w of waiting) {
+          feature.subfeatures.push(w)
         }
+        orphans.delete(id)
       }
     }
 

src/util.ts

@@ -2,7 +2,6 @@
 // JavaScript port of Robert Buels's Bio::GFF3::LowLevel Perl module.
 
 const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/
-const lineEndRegex = /\r?\n$/
 const whitespaceRegex = /\s+/
 const nonDigitRegex = /\D/g
 
@@ -252,25 +251,24 @@ export function parseDirective(
     return null
   }
 
-  const [, name] = match
-  let [, , contents] = match
+  const name = match[1]!
+  let contents = match[2]!
 
-  const parsed: GFF3Directive = { directive: name! }
-  if (contents!.length) {
-    contents = contents!.replace(lineEndRegex, '')
-    parsed.value = contents
+  const parsed: GFF3Directive = { directive: name }
+  if (contents.length) {
+    parsed.value = contents.trimEnd()
   }
 
   if (name === 'sequence-region') {
-    const c = contents!.split(whitespaceRegex, 3)
+    const c = contents.split(whitespaceRegex, 3)
     return {
       ...parsed,
       seq_id: c[0]!,
       start: c[1]!.replaceAll(nonDigitRegex, ''),
       end: c[2]!.replaceAll(nonDigitRegex, ''),
     }
   } else if (name === 'genome-build') {
-    const [source, buildName] = contents!.split(whitespaceRegex, 2)
+    const [source, buildName] = contents.split(whitespaceRegex, 2)
     return {
       ...parsed,
       source: source!,
@@ -446,11 +444,6 @@ function parseAttributesJBrowseImpl(
       const eqIdx = attrString.indexOf('=', start)
       if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
         const tag = attrString.slice(start, eqIdx)
-        if (tag === '_lineHash') {
-          start = semiIdx + 1
-          continue
-        }
-
         let key = COMMON_ATTRS[tag]
         if (key === undefined) {
           key = tag.toLowerCase()