@apollo-annotation/shared 0.3.9 → 0.3.11

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.9",
+  "version": "0.3.11",
   "main": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
@@ -10,9 +10,9 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.9",
-    "@apollo-annotation/mst": "^0.3.9",
-    "@apollo-annotation/schemas": "^0.3.9",
+    "@apollo-annotation/common": "^0.3.11",
+    "@apollo-annotation/mst": "^0.3.11",
+    "@apollo-annotation/schemas": "^0.3.11",
     "@gmod/gff": "^2.0.0",
     "@gmod/indexedfasta": "^2.0.4",
     "@jbrowse/core": "^3.6.5",

package/src/Changes/AddFeatureChange.ts

@@ -89,6 +89,12 @@ export class AddFeatureChange extends FeatureChange {
     let featureCnt = 0
     logger.debug?.(`changes: ${JSON.stringify(changes)}`)
 
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
+    }
+
     // Loop the changes
     for (const change of changes) {
       logger.debug?.(`change: ${JSON.stringify(change)}`)
@@ -106,9 +112,10 @@ export class AddFeatureChange extends FeatureChange {
 
       // CopyFeature is called from CopyFeature.tsx
       if (copyFeature) {
+        const indexedIds = this.getIndexedIds(addedFeature, idsToIndex)
         // Add into Mongo
         const [newFeatureDoc] = await featureModel.create(
-          [{ ...addedFeature, allIds, status: -1, user }],
+          [{ ...addedFeature, allIds, indexedIds, status: -1, user }],
           { session },
         )
         logger.debug?.(
@@ -116,6 +123,7 @@ export class AddFeatureChange extends FeatureChange {
         )
         featureCnt++
       } else {
+        const indexedIds = this.getIndexedIds(addedFeature, idsToIndex)
         // Adding new child feature
         if (parentFeatureId) {
           const topLevelFeature = await featureModel
@@ -139,12 +147,16 @@ export class AddFeatureChange extends FeatureChange {
           this.addChild(parentFeature, addedFeature)
           const childIds = this.getChildFeatureIds(addedFeature)
           topLevelFeature.allIds.push(_id, ...childIds)
+          if (indexedIds.length > 0 && !topLevelFeature.indexedIds) {
+            topLevelFeature.indexedIds = []
+          }
+          topLevelFeature.indexedIds?.push(...indexedIds)
           await topLevelFeature.save()
         } else {
           const childIds = this.getChildFeatureIds(addedFeature)
           const allIdsV2 = [_id, ...childIds]
           const [newFeatureDoc] = await featureModel.create(
-            [{ allIds: allIdsV2, status: 0, ...addedFeature }],
+            [{ allIds: allIdsV2, indexedIds, status: 0, ...addedFeature }],
             { session },
           )
           logger.verbose?.(`Added docId "${newFeatureDoc._id}"`)

package/src/Changes/DeleteFeatureChange.ts

@@ -67,6 +67,12 @@ export class DeleteFeatureChange extends FeatureChange {
     const { featureModel, session } = backend
     const { changes, logger } = this
 
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
+    }
+
     // Loop the changes
     for (const change of changes) {
       const { deletedFeature, parentFeatureId } = change
@@ -105,6 +111,18 @@ export class DeleteFeatureChange extends FeatureChange {
       featureDoc.allIds = featureDoc.allIds.filter(
         (id) => !deletedIds.includes(id),
       )
+      const indexedIds = this.getIndexedIds(featureDoc, idsToIndex)
+      if (featureDoc.indexedIds) {
+        if (indexedIds.length > 0) {
+          featureDoc.indexedIds = indexedIds
+        } else {
+          delete featureDoc.indexedIds
+        }
+      } else {
+        if (indexedIds.length > 0) {
+          featureDoc.indexedIds = indexedIds
+        }
+      }
       // Save updated document in Mongo
       featureDoc.markModified('children') // Mark as modified. Without this save() -method is not updating data in database
       try {

package/src/Changes/FeatureAttributeChange.ts

@@ -100,11 +100,24 @@ export class FeatureAttributeChange extends FeatureChange {
       featuresForChanges.push({ feature: foundFeature, topLevelFeature })
     }
 
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
+    }
     // Let's update objects
     for (const [idx, change] of changes.entries()) {
       const { newAttributes } = change
       const { feature, topLevelFeature } = featuresForChanges[idx]
+      const indexedIdsChanged = idsToIndex?.some(
+        (id) => id in newAttributes || id in (feature?.attributes ?? {}),
+      )
       feature.attributes = newAttributes
+      if (indexedIdsChanged) {
+        const indexedIds = this.getIndexedIds(topLevelFeature, idsToIndex)
+        topLevelFeature.indexedIds = indexedIds
+        topLevelFeature.markModified('indexedIds')
+      }
       if (topLevelFeature._id.equals(feature._id)) {
         topLevelFeature.markModified('attributes') // Mark as modified. Without this save() -method is not updating data in database
       } else {

package/src/Changes/FromFileBaseChange.ts

@@ -4,6 +4,7 @@ import {
   AssemblySpecificChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import {
   type FileDocument,
   type RefSeqDocument,
@@ -183,8 +184,13 @@ export abstract class FromFileBaseChange extends AssemblySpecificChange {
   }
 
   async addFeatureIntoDb(gff3Feature: GFF3Feature, backend: ServerDataStore) {
-    const { featureModel, refSeqModel, user } = backend
+    const { INDEXED_IDS } = process.env
+    let idsToIndex: string[] | undefined
+    if (INDEXED_IDS) {
+      idsToIndex = INDEXED_IDS.split(',')
+    }
     const { assembly, refSeqCache } = this
+    const { featureModel, refSeqModel, user } = backend
 
     const [{ seq_id: refName }] = gff3Feature
     if (!refName) {
@@ -206,19 +212,25 @@ export abstract class FromFileBaseChange extends AssemblySpecificChange {
         `RefSeq was not found by assembly "${assembly}" and seq_id "${refName}" not found`,
       )
     }
-    // Let's add featureId to parent feature
-    const featureIds: string[] = []
-
-    const newFeature = gff3ToAnnotationFeature(
-      gff3Feature,
-      refSeqDoc._id,
-      featureIds,
-    )
+    const newFeature = gff3ToAnnotationFeature(gff3Feature, refSeqDoc._id)
+    const allIds = this.getAllIds(newFeature)
+    const indexedIds = this.getIndexedIds(newFeature, idsToIndex)
 
     // Add into Mongo
     // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
     await featureModel.create([
-      { allIds: featureIds, ...newFeature, user, status: -1 },
+      { allIds, indexedIds, ...newFeature, user, status: -1 },
     ])
   }
+
+  getAllIds(feature: AnnotationFeatureSnapshot): string[] {
+    const allIds = [feature._id]
+    if (feature.children) {
+      for (const child of Object.values(feature.children)) {
+        const childIds = this.getAllIds(child)
+        allIds.push(...childIds)
+      }
+    }
+    return allIds
+  }
 }

package/src/GFF3/annotationFeatureToGFF3.test.ts

@@ -1,12 +1,34 @@
 /* eslint-disable prefer-destructuring */
 /* eslint-disable @typescript-eslint/no-floating-promises */
+import { readFileSync } from 'node:fs'
 import { describe, it } from 'node:test'
 
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { assert } from 'chai'
+import { formatSync } from '@gmod/gff'
+import { assert, expect } from 'chai'
 
 import { annotationFeatureToGFF3 } from './annotationFeatureToGFF3'
-import { readAnnotationFeatureSnapshot } from './gff3ToAnnotationFeature.test'
+import { readAnnotationFeatureSnapshot, testCases } from './testUtil'
+
+describe('Converts AnnotationFeatureSnapshot JSON to GFF3 when', () => {
+  for (const testCase of testCases) {
+    const { filenameStem, description } = testCase
+    it(description, () => {
+      const annotationFeatures = JSON.parse(
+        readFileSync(`test_data/${filenameStem}.json`, 'utf8'),
+      ) as AnnotationFeatureSnapshot[]
+      const expectedGFF3 = readFileSync(
+        `test_data/${filenameStem}.gff3`,
+        'utf8',
+      )
+      const gffFeatures = annotationFeatures.map((annotationFeature) =>
+        annotationFeatureToGFF3(annotationFeature),
+      )
+      const gff3 = formatSync(gffFeatures)
+      expect(gff3).to.equal(expectedGFF3)
+    })
+  }
+})
 
 describe('annotationFeatureToGFF3', () => {
   it('Test mandatory columns', () => {

package/src/GFF3/gff3ToAnnotationFeature.test.ts

@@ -8,77 +8,10 @@ import { assert, use } from 'chai'
 import chaiExclude from 'chai-exclude'
 
 import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature'
+import { readAnnotationFeatureSnapshot, testCases } from './testUtil'
 
 use(chaiExclude)
 
-const testCases: [string, string, AnnotationFeatureSnapshot][] = [
-  [
-    'a feature with no children',
-    'ctgA	example	remark	1000	2000	.	.	.	Name=Remark:hga;Alias=hga\n',
-    {
-      _id: '66c51f3e002c683eaf98a223',
-      refSeq: 'ctgA',
-      type: 'remark',
-      min: 999,
-      max: 2000,
-      attributes: {
-        gff_source: ['example'],
-        gff_name: ['Remark:hga'],
-        gff_alias: ['hga'],
-      },
-    },
-  ],
-  [
-    'a feature with two children',
-    `ctgA	est	EST_match	1050	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 1 654
-ctgA	est	match_part	1050	1500	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 1 451
-ctgA	est	match_part	3000	3202	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 452 654
-`,
-    {
-      _id: '66cf9fbb4e947fa2c27d3d6a',
-      refSeq: 'ctgA',
-      type: 'EST_match',
-      min: 1049,
-      max: 3202,
-      strand: 1,
-      children: {
-        '66cf9fbb4e947fa2c27d3d68': {
-          _id: '66cf9fbb4e947fa2c27d3d68',
-          refSeq: 'ctgA',
-          type: 'match_part',
-          min: 1049,
-          max: 1500,
-          strand: 1,
-          attributes: {
-            gff_source: ['est'],
-            gff_name: ['agt830.5'],
-            gff_target: ['agt830.5 1 451'],
-          },
-        },
-        '66cf9fbb4e947fa2c27d3d69': {
-          _id: '66cf9fbb4e947fa2c27d3d69',
-          refSeq: 'ctgA',
-          type: 'match_part',
-          min: 2999,
-          max: 3202,
-          strand: 1,
-          attributes: {
-            gff_source: ['est'],
-            gff_name: ['agt830.5'],
-            gff_target: ['agt830.5 452 654'],
-          },
-        },
-      },
-      attributes: {
-        gff_source: ['est'],
-        gff_id: ['Match1'],
-        gff_name: ['agt830.5'],
-        gff_target: ['agt830.5 1 654'],
-      },
-    },
-  ],
-]
-
 interface AnnotationFeatureSnapshotWithChildrenArray
   extends Omit<AnnotationFeatureSnapshot, 'children'> {
   children?: AnnotationFeatureSnapshotWithChildrenArray[]
@@ -108,6 +41,29 @@ function compareFeatures(
   )
 }
 
+describe('Converts GFF3 to AnnotationFeatureSnapshot JSON when', () => {
+  for (const testCase of testCases) {
+    const { filenameStem, description } = testCase
+    it(description, () => {
+      const fileText = readFileSync(`test_data/${filenameStem}.gff3`, 'utf8')
+      const gffFeatures = parseStringSync(fileText, { parseSequences: false })
+      const annotationFeatures = gffFeatures.map((gff3Feature) =>
+        gff3ToAnnotationFeature(gff3Feature),
+      )
+      const annotationFeaturesExpected = JSON.parse(
+        readFileSync(`test_data/${filenameStem}.json`, 'utf8'),
+      ) as AnnotationFeatureSnapshot[]
+      for (const [
+        i,
+        annotationFeatureExpected,
+      ] of annotationFeaturesExpected.entries()) {
+        const annotationFeature = annotationFeatures[i]
+        compareFeatures(annotationFeature, annotationFeatureExpected)
+      }
+    })
+  }
+})
+
 function readFeatureFile(fn: string): GFF3Feature[] {
   const lines = readFileSync(fn).toString().split('\n')
   const feature: string[] = []
@@ -120,13 +76,6 @@ function readFeatureFile(fn: string): GFF3Feature[] {
   return inGff
 }
 
-export function readAnnotationFeatureSnapshot(
-  fn: string,
-): AnnotationFeatureSnapshot {
-  const lines = readFileSync(fn).toString()
-  return JSON.parse(lines) as AnnotationFeatureSnapshot
-}
-
 const [ex1, , ex2, , ex3, , ex4] = readFeatureFile(
   'test_data/gene_representations.gff3',
 )
@@ -139,13 +88,6 @@ describe('gff3ToAnnotationFeature examples', () => {
     const expected = readAnnotationFeatureSnapshot('test_data/one_cds.json')
     compareFeatures(actual, expected)
   })
-  it('Convert two CDSs', () => {
-    const actual = gff3ToAnnotationFeature(
-      readFeatureFile('test_data/two_cds.gff3')[0],
-    )
-    const expected = readAnnotationFeatureSnapshot('test_data/two_cds.json')
-    compareFeatures(actual, expected)
-  })
   it('Convert example 1', () => {
     const actual = gff3ToAnnotationFeature(ex1)
     const txt = JSON.stringify(actual, null, 2)
@@ -228,19 +170,6 @@ describe('CDS without exons', () => {
   })
 })
 
-describe('gff3ToAnnotationFeature', () => {
-  for (const testCase of testCases) {
-    const [description, featureLine, convertedFeature] = testCase
-    it(`converts ${description}`, () => {
-      const gff3Feature = parseStringSync(featureLine, {
-        parseSequences: false,
-      })
-      const feature = gff3ToAnnotationFeature(gff3Feature[0])
-      compareFeatures(convertedFeature, feature)
-    })
-  }
-})
-
 describe('Source and score', () => {
   it('Convert score and source', () => {
     const gffFeature: GFF3Feature = [

package/src/GFF3/gff3ToAnnotationFeature.ts

@@ -8,7 +8,6 @@ import { gffToInternal, isGFFReservedAttribute } from './gffReservedKeys'
 export function gff3ToAnnotationFeature(
   gff3Feature: GFF3Feature,
   refSeq?: string,
-  featureIds?: string[],
 ): AnnotationFeatureSnapshot {
   const [firstFeature] = gff3Feature
   const { end, seq_id: refName, start, strand, type } = firstFeature
@@ -35,7 +34,7 @@ export function gff3ToAnnotationFeature(
 
   const [min, max] = getFeatureMinMax(gff3Feature)
 
-  const convertedChildren = convertChildren(gff3Feature, refSeq, featureIds)
+  const convertedChildren = convertChildren(gff3Feature, refSeq)
 
   const convertedAttributes = convertFeatureAttributes(gff3Feature)
 
@@ -61,9 +60,6 @@ export function gff3ToAnnotationFeature(
   if (convertedAttributes) {
     feature.attributes = convertedAttributes
   }
-  if (featureIds) {
-    featureIds.push(feature._id)
-  }
   return feature
 }
 
@@ -182,13 +178,13 @@ function convertChildren(
     if (firstChildFeatureLocation.type === 'CDS') {
       cdsFeatures.push(childFeature)
     } else {
-      const child = gff3ToAnnotationFeature(childFeature, refSeq, featureIds)
+      const child = gff3ToAnnotationFeature(childFeature, refSeq)
       convertedChildren[child._id] = child
     }
   }
 
   if (cdsFeatures.length > 0) {
-    const processedCDS = processCDS(cdsFeatures, refSeq, featureIds)
+    const processedCDS = processCDS(cdsFeatures, refSeq)
 
     for (const cds of processedCDS) {
       convertedChildren[cds._id] = cds
@@ -372,16 +368,13 @@ function mergeAnnotationFeatures(
 function processCDS(
   cdsFeatures: GFF3Feature[],
   refSeq?: string,
-  featureIds?: string[],
 ): AnnotationFeatureSnapshot[] {
   const locationCounts = cdsFeatures.map((cds) => cds.length)
   // If any CDS have multiple locations, assume it really is multiple CDS
   // (e.g. the mRNA has multiple alternative translational start sites)
   // and process normally.
   if (locationCounts.some((count) => count > 1)) {
-    return cdsFeatures.map((cds) =>
-      gff3ToAnnotationFeature(cds, refSeq, featureIds),
-    )
+    return cdsFeatures.map((cds) => gff3ToAnnotationFeature(cds, refSeq))
   }
   // If all CDS have a single location, we guess that this GFF3 represented CDS
   // as multiple features instead of a single feature with multiple locations.
@@ -402,7 +395,7 @@ function processCDS(
   })
   // If no overlaps, assume it's a single CDS feature
   if (!overlapping) {
-    return [gff3ToAnnotationFeature(sortedCDSLocations, refSeq, featureIds)]
+    return [gff3ToAnnotationFeature(sortedCDSLocations, refSeq)]
   }
   // Some CDS locations overlap, the best we can do is use the original order to
   // guess how to group the locations into features
@@ -430,7 +423,5 @@ function processCDS(
       lastGroup.push(location)
     }
   }
-  return groupedLocations.map((group) =>
-    gff3ToAnnotationFeature(group, refSeq, featureIds),
-  )
+  return groupedLocations.map((group) => gff3ToAnnotationFeature(group, refSeq))
 }

package/src/GFF3/testUtil.ts

@@ -0,0 +1,25 @@
+import { readFileSync } from 'node:fs'
+
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+
+export function readAnnotationFeatureSnapshot(
+  fn: string,
+): AnnotationFeatureSnapshot {
+  const lines = readFileSync(fn).toString()
+  return JSON.parse(lines) as AnnotationFeatureSnapshot
+}
+
+export const testCases: { filenameStem: string; description: string }[] = [
+  {
+    filenameStem: 'single_feature_no_children',
+    description: 'there is a single feature with no children',
+  },
+  {
+    filenameStem: 'single_feature_two_children',
+    description: 'there is a single feature with two children',
+  },
+  {
+    filenameStem: 'gene_with_two_cds',
+    description: 'Gene with two CDS',
+  },
+]

package/test_data/gene_with_two_cds.gff3

@@ -0,0 +1,6 @@
+chr1	.	gene	1000	9000	.	+	.	testid=t003;ID=gene10001;Name=EDEN
+chr1	.	mRNA	1050	9000	.	+	.	testid=t004,t001,t004;Parent=gene10001;ID=mRNA10001;Name=EDEN.1
+chr1	.	exon	1050	1500	.	+	.	testid=t007;Parent=mRNA10001;ID=exon10001
+chr1	.	exon	5000	5500	.	+	.	testid=t010;Parent=mRNA10001;ID=exon10004
+chr1	.	CDS	1201	1500	.	+	0	testid=t012,t013,t014;Parent=mRNA10001;ID=cds10001;Name=edenprotein.1
+chr1	.	CDS	5000	5000	.	+	0	testid=t012,t013,t014;Parent=mRNA10001;ID=cds10001;Name=edenprotein.1

package/test_data/gene_with_two_cds.json

@@ -0,0 +1,69 @@
+[
+  {
+    "_id": "66d70f3b9c7a7460925687a3",
+    "refSeq": "chr1",
+    "type": "gene",
+    "min": 999,
+    "max": 9000,
+    "strand": 1,
+    "children": {
+      "66d70f3b9c7a7460925687a2": {
+        "_id": "66d70f3b9c7a7460925687a2",
+        "refSeq": "chr1",
+        "type": "mRNA",
+        "min": 1049,
+        "max": 9000,
+        "strand": 1,
+        "children": {
+          "66d70f3b9c7a74609256879f": {
+            "_id": "66d70f3b9c7a74609256879f",
+            "refSeq": "chr1",
+            "type": "exon",
+            "min": 1049,
+            "max": 1500,
+            "strand": 1,
+            "attributes": {
+              "testid": ["t007"],
+              "gff_id": ["exon10001"]
+            }
+          },
+          "66d70f3b9c7a7460925687a0": {
+            "_id": "66d70f3b9c7a7460925687a0",
+            "refSeq": "chr1",
+            "type": "exon",
+            "min": 4999,
+            "max": 5500,
+            "strand": 1,
+            "attributes": {
+              "testid": ["t010"],
+              "gff_id": ["exon10004"]
+            }
+          },
+          "66d70f3b9c7a7460925687a1": {
+            "_id": "66d70f3b9c7a7460925687a1",
+            "refSeq": "chr1",
+            "type": "CDS",
+            "min": 1200,
+            "max": 5000,
+            "strand": 1,
+            "attributes": {
+              "testid": ["t012", "t013", "t014"],
+              "gff_id": ["cds10001"],
+              "gff_name": ["edenprotein.1"]
+            }
+          }
+        },
+        "attributes": {
+          "testid": ["t004", "t001", "t004"],
+          "gff_id": ["mRNA10001"],
+          "gff_name": ["EDEN.1"]
+        }
+      }
+    },
+    "attributes": {
+      "testid": ["t003"],
+      "gff_id": ["gene10001"],
+      "gff_name": ["EDEN"]
+    }
+  }
+]

package/test_data/single_feature_no_children.gff3

@@ -0,0 +1 @@
+ctgA	example	remark	1000	2000	.	.	.	Name=Remark:hga;Alias=hga

package/test_data/single_feature_no_children.json

@@ -0,0 +1,14 @@
+[
+  {
+    "_id": "6931ef3bf5c33f70085c3a7b",
+    "refSeq": "ctgA",
+    "type": "remark",
+    "min": 999,
+    "max": 2000,
+    "attributes": {
+      "gff_source": ["example"],
+      "gff_name": ["Remark:hga"],
+      "gff_alias": ["hga"]
+    }
+  }
+]

package/test_data/single_feature_two_children.gff3

@@ -0,0 +1,3 @@
+ctgA	est	EST_match	1050	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 1 654
+ctgA	est	match_part	1050	1500	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 1 451
+ctgA	est	match_part	3000	3202	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 452 654

package/test_data/single_feature_two_children.json

@@ -0,0 +1,44 @@
+[
+  {
+    "_id": "6931fc4f88722ca882ba334c",
+    "refSeq": "ctgA",
+    "type": "EST_match",
+    "min": 1049,
+    "max": 3202,
+    "strand": 1,
+    "children": {
+      "6931fc4f88722ca882ba334a": {
+        "_id": "6931fc4f88722ca882ba334a",
+        "refSeq": "ctgA",
+        "type": "match_part",
+        "min": 1049,
+        "max": 1500,
+        "strand": 1,
+        "attributes": {
+          "gff_source": ["est"],
+          "gff_name": ["agt830.5"],
+          "gff_target": ["agt830.5 1 451"]
+        }
+      },
+      "6931fc4f88722ca882ba334b": {
+        "_id": "6931fc4f88722ca882ba334b",
+        "refSeq": "ctgA",
+        "type": "match_part",
+        "min": 2999,
+        "max": 3202,
+        "strand": 1,
+        "attributes": {
+          "gff_source": ["est"],
+          "gff_name": ["agt830.5"],
+          "gff_target": ["agt830.5 452 654"]
+        }
+      }
+    },
+    "attributes": {
+      "gff_source": ["est"],
+      "gff_id": ["Match1"],
+      "gff_name": ["agt830.5"],
+      "gff_target": ["agt830.5 1 654"]
+    }
+  }
+]

package/test_data/two_cds.gff3

@@ -1,9 +0,0 @@
-##gff-version 3
-##sequence-region   chr1 1000 9000
-#example01
-chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN;testid=t003
-chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004,t001,t004
-chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001;testid=t007
-chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001;testid=t010
-chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t012,t013,t014
-chr1	.	CDS	5000	5000	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t014