Non-streaming parsers

plugins/gff3/package.json

@@ -38,7 +38,7 @@
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/gff": "^1.3.0",
+    "gff-nostream": "^1.3.3",
     "@gmod/tabix": "^1.5.6"
   },
   "peerDependencies": {

plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts

@@ -8,7 +8,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import IntervalTree from '@flatten-js/interval-tree'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
 import { unzip } from '@gmod/bgzf-filehandle'
-import gff from '@gmod/gff'
+import { parseStringSync } from 'gff-nostream'
 import { isGzip, updateStatus } from '@jbrowse/core/util'
 
 import { featureData } from '../featureData'
@@ -76,14 +76,13 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
           if (!this.calculatedIntervalTreeMap[refName]) {
             sc?.('Parsing GFF data')
             const intervalTree = new IntervalTree()
-            gff
-              .parseStringSync(lines, {
-                parseFeatures: true,
-                parseComments: false,
-                parseDirectives: false,
-                parseSequences: false,
-                disableDerivesFromReferences: true,
-              })
+            parseStringSync(lines, {
+              parseFeatures: true,
+              parseComments: false,
+              parseDirectives: false,
+              parseSequences: false,
+              disableDerivesFromReferences: true,
+            })
               .flat()
               .map(
                 (f, i) =>

plugins/gff3/src/Gff3TabixAdapter/Gff3TabixAdapter.ts

@@ -8,7 +8,7 @@ import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
 import { TabixIndexedFile } from '@gmod/tabix'
-import gff, { GFF3Feature } from '@gmod/gff'
+import { parseStringSync, GFF3Feature } from 'gff-nostream'
 import { Observer } from 'rxjs'
 import {
   readConfObject,
@@ -124,7 +124,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
       }
 
       const gff3 = lines
-        .map((lineRecord: LineFeature) => {
+        .map(lineRecord => {
           if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
             if (!lineRecord.fields[8].includes('_lineHash')) {
               lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`
@@ -136,27 +136,28 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
         })
         .join('\n')
 
-      const features = gff.parseStringSync(gff3, {
-        parseFeatures: true,
-        parseComments: false,
-        parseDirectives: false,
-        parseSequences: false,
-        disableDerivesFromReferences: true,
-      })
-
-      features.forEach(featureLocs => {
-        this.formatFeatures(featureLocs).forEach(f => {
-          if (
-            doesIntersect2(
-              f.get('start'),
-              f.get('end'),
-              originalQuery.start,
-              originalQuery.end,
-            )
-          ) {
-            observer.next(f)
-          }
-        })
+      parseStringSync(gff3).forEach(featureLocs => {
+        console.log({ featureLocs })
+        featureLocs
+          .map(
+            featureLoc =>
+              new SimpleFeature({
+                data: featureData(featureLoc),
+                id: `${this.id}-offset-${featureLoc.attributes?._lineHash?.[0]}`,
+              }),
+          )
+          .forEach(f => {
+            if (
+              doesIntersect2(
+                f.get('start'),
+                f.get('end'),
+                originalQuery.start,
+                originalQuery.end,
+              )
+            ) {
+              observer.next(f)
+            }
+          })
       })
       observer.complete()
     } catch (e) {
@@ -180,15 +181,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     }
   }
 
-  private formatFeatures(featureLocs: GFF3Feature) {
-    return featureLocs.map(
-      featureLoc =>
-        new SimpleFeature({
-          data: featureData(featureLoc),
-          id: `${this.id}-offset-${featureLoc.attributes?._lineHash?.[0]}`,
-        }),
-    )
-  }
-
   public freeResources(/* { region } */) {}
 }

plugins/gff3/src/featureData.ts

@@ -1,4 +1,4 @@
-import { GFF3FeatureLineWithRefs } from '@gmod/gff'
+import { GFF3FeatureLineWithRefs } from 'gff-nostream'
 
 export function featureData(data: GFF3FeatureLineWithRefs) {
   const f: Record<string, unknown> = { ...data }

plugins/gtf/package.json

@@ -38,7 +38,7 @@
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/gtf": "^0.0.9"
+    "gtf-nostream": "^1.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",

plugins/gtf/src/GtfAdapter/GtfAdapter.ts

@@ -13,7 +13,7 @@ import {
   isGzip,
 } from '@jbrowse/core/util'
 import { unzip } from '@gmod/bgzf-filehandle'
-import gtf from '@gmod/gtf'
+import { parseStringSync } from 'gtf-nostream'
 
 // locals
 import { FeatureLoc, featureData } from '../util'
@@ -83,7 +83,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
             sc?.('Parsing GTF data')
             const intervalTree = new IntervalTree()
             ;(
-              gtf.parseStringSync(lines, {
+              parseStringSync(lines, {
                 parseFeatures: true,
                 parseComments: false,
                 parseDirectives: false,

yarn.lock

@@ -2333,20 +2333,6 @@
     pump "^3.0.0"
     split2 "^4.2.0"
 
-"@gmod/gff@^1.3.0":
-  version "1.3.0"
-  resolved "https://registry.yarnpkg.com/@gmod/gff/-/gff-1.3.0.tgz#d231a6f807cfb8f191c26c6410021c17155e4093"
-  integrity sha512-OjEnQLR6iIcrau603blFfUkmnWGDVfOu/LQoJNa7TsvKnjWlHYPlvqb5h2IV7wI+zElDY648mQ9zrElt2uR80A==
-  dependencies:
-    stream-browserify "^3.0.0"
-
-"@gmod/gtf@^0.0.9":
-  version "0.0.9"
-  resolved "https://registry.yarnpkg.com/@gmod/gtf/-/gtf-0.0.9.tgz#87ef1e753ab2e9903affdd97454e6f948da38cd4"
-  integrity sha512-IPqKOg8e9nUvxI+8mJznKXdWMrErseJx/w+HnrU+ePTWzr2uCa8iHcbVzfSlPgqxWKkQ15/lK4BnUJSnQHfVow==
-  dependencies:
-    stream-browserify "^3.0.0"
-
 "@gmod/http-range-fetcher@^3.0.4":
   version "3.0.4"
   resolved "https://registry.yarnpkg.com/@gmod/http-range-fetcher/-/http-range-fetcher-3.0.4.tgz#7ab2fdc96703b9f977d9c517e8028fb68765e118"
@@ -9439,6 +9425,11 @@ get-value@^3.0.1:
   dependencies:
     isobject "^3.0.1"
 
+gff-nostream@^1.3.3:
+  version "1.3.3"
+  resolved "https://registry.yarnpkg.com/gff-nostream/-/gff-nostream-1.3.3.tgz#bd1ed4436a3826051dd91eec6a9034349b263ab0"
+  integrity sha512-SwwpN+2jxaeherEC4PZPnsL2rsD3kUev+NT9jJJj+pg7kiYQDu7W4B4QzFcJUf7dUvuqWSNie2Nx8xb7u7s//Q==
+
 giget@^1.0.0:
   version "1.2.3"
   resolved "https://registry.yarnpkg.com/giget/-/giget-1.2.3.tgz#ef6845d1140e89adad595f7f3bb60aa31c672cb6"
@@ -9705,6 +9696,11 @@ graphemer@^1.4.0:
   resolved "https://registry.yarnpkg.com/graphemer/-/graphemer-1.4.0.tgz#fb2f1d55e0e3a1849aeffc90c4fa0dd53a0e66c6"
   integrity sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==
 
+gtf-nostream@^1.0.0:
+  version "1.3.2"
+  resolved "https://registry.yarnpkg.com/gtf-nostream/-/gtf-nostream-1.3.2.tgz#6cc9d13de26f7615ffaa5263462b3b195bbe7b0b"
+  integrity sha512-o8bqFWoZ7JjkKfpVOCyhFsW3dAr4gR15khm39Z9PXuymesoDaMDn6AW4m+L69nBWd3JAL5xFxr7mSslFsCu6sg==
+
 gzip-size@^6.0.0:
   version "6.0.0"
   resolved "https://registry.yarnpkg.com/gzip-size/-/gzip-size-6.0.0.tgz#065367fd50c239c0671cbcbad5be3e2eeb10e462"
@@ -10177,7 +10173,7 @@ inflight@^1.0.4:
     once "^1.3.0"
     wrappy "1"
 
-inherits@2, inherits@2.0.4, inherits@^2.0.1, inherits@^2.0.3, inherits@^2.0.4, inherits@~2.0.3, inherits@~2.0.4:
+inherits@2, inherits@2.0.4, inherits@^2.0.1, inherits@^2.0.3, inherits@^2.0.4, inherits@~2.0.3:
   version "2.0.4"
   resolved "https://registry.yarnpkg.com/inherits/-/inherits-2.0.4.tgz#0fa2c64f932917c3433a0ded55363aae37416b7c"
   integrity sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ==
@@ -14135,7 +14131,7 @@ readable-stream@^2.0.1, readable-stream@^2.3.0, readable-stream@^2.3.5, readable
     string_decoder "~1.1.1"
     util-deprecate "~1.0.1"
 
-readable-stream@^3.0.0, readable-stream@^3.0.2, readable-stream@^3.0.6, readable-stream@^3.1.1, readable-stream@^3.4.0, readable-stream@^3.5.0, readable-stream@^3.6.0:
+readable-stream@^3.0.0, readable-stream@^3.0.2, readable-stream@^3.0.6, readable-stream@^3.1.1, readable-stream@^3.4.0, readable-stream@^3.6.0:
   version "3.6.2"
   resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-3.6.2.tgz#56a9b36ea965c00c5a93ef31eb111a0f11056967"
   integrity sha512-9u/sniCrY3D5WdsERHzHE4G2YCXqoG5FTHUiCC4SIbr6XcLZBY05ya9EKjYek9O5xOAwjGq+1JdGBAS7Q9ScoA==
@@ -15158,14 +15154,6 @@ storybook@^8.0.0:
     tiny-invariant "^1.3.1"
     ts-dedent "^2.0.0"
 
-stream-browserify@^3.0.0:
-  version "3.0.0"
-  resolved "https://registry.yarnpkg.com/stream-browserify/-/stream-browserify-3.0.0.tgz#22b0a2850cdf6503e73085da1fc7b7d0c2122f2f"
-  integrity sha512-H73RAHsVBapbim0tU2JwwOiXUj+fikfiaoYAKHF3VJfA0pe2BCzkhAHBlLG6REzE+2WNZcxOXjK7lkso+9euLA==
-  dependencies:
-    inherits "~2.0.4"
-    readable-stream "^3.5.0"
-
 string-length@^4.0.1:
   version "4.0.2"
   resolved "https://registry.yarnpkg.com/string-length/-/string-length-4.0.2.tgz#a8a8dc7bd5c1a82b9b3c8b87e125f66871b6e57a"