Merge pull request #4 from luizirber/lirber/seqparser

Parse sequences in Rust/wasm

package.json

@@ -1,6 +1,6 @@
 {
   "name": "mgnify-sourmash-component",
-  "version": "0.2.4",
+  "version": "0.3.0",
   "description": "A web component to select FastA file and generate sourmash signatures locally.",
   "module": "dist/mgnify-sourmash-component.js",
   "main": "dist/mgnify-sourmash-component.js",
@@ -24,8 +24,6 @@
   "author": "Gustavo A. Salazar",
   "license": "ISC",
   "devDependencies": {
-    "@types/pumpify": "1.4.1",
-    "@types/through2": "2.0.36",
     "@typescript-eslint/eslint-plugin": "4.31.0",
     "@typescript-eslint/parser": "4.31.0",
     "eslint": "7.32.0",
@@ -37,25 +35,16 @@
     "prettier": "2.4.0",
     "ts-loader": "9.2.5",
     "typescript": "4.4.2",
-    "webpack": "5.52.1",
+    "webpack": "^5.90.3",
     "webpack-cli": "4.8.0",
-    "webpack-dev-server": "4.2.0"
+    "webpack-dev-server": "^4.15.1"
   },
   "dependencies": {
     "bl": "5.0.0",
-    "buffer": "6.0.3",
-    "buffer-from": "1.1.2",
-    "duplexify": "4.1.2",
-    "fastqstream": "0.1.0",
-    "filestream": "5.0.0",
     "lit": "2.0.0-rc.2",
     "lit-css-loader": "1.0.1",
     "process": "0.11.10",
-    "pumpify": "2.0.1",
-    "sourmash": "0.11.0",
-    "split": "1.0.1",
-    "stream": "0.0.2",
-    "through2": "4.0.2",
+    "sourmash": "0.13.1",
     "util": "0.12.4",
     "worker-loader": "3.0.8"
   }

src/custom.d.ts

@@ -4,15 +4,6 @@ declare module '*.css' {
   export default content;
 }
 
-interface Read {
-  // eslint-disable-next-line  @typescript-eslint/no-misused-new
-  new (file: File): Read;
-  reader: {
-    onprogress: (data: any) => void;
-  };
-  pipe: (f: () => any) => any;
-}
-
 interface KmerMinHashOptions {
   num: number;
   ksize: number;
@@ -24,20 +15,6 @@ interface KmerMinHashOptions {
   track_abundance: boolean;
 }
 
-type DataChunk = Uint8Array | Uint16Array | Uint32Array;
-
-declare module 'filestream' {
-  export const read: Read;
-}
-
-type SwapFuntion = (_: any, x?: any) => any;
-
-// declare module 'fasta-parser' {
-//   import { Stream } from 'stream';
-//   const Fasta: () => Stream;
-//   export default Fasta;
-// }
-
 declare module '*.worker.ts' {
   // You need to change `Worker`, if you specified a different value for the `workerType` option
   class WebpackWorker extends Worker {

src/index.ts

@@ -8,7 +8,7 @@ import style from './index.css';
 
 const worker = new Worker();
 
-const SUPPORTED_EXTENSIONS = ['.fa', '.fasta', '.fna'];
+const SUPPORTED_EXTENSIONS = ['.fa', '.fasta', '.fna', '.gz', '.fq', '.fastq'];
 @customElement('mgnify-sourmash-component')
 export class MGnifySourmash extends LitElement {
   @property({ type: Boolean, reflect: true })