Index-debug

GMOD · Aug 8, 2024 · c5178f3 · c5178f3
1 parent 8ac9191
commit c5178f3
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Showing 6 changed files with 177 additions and 138 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -15,9 +15,6 @@ const compat = new FlatCompat({
 })
 
 export default [
-  {
-    ignores: ['src/binary-parser/*.js'],
-  },
   ...compat.extends(
     'plugin:@typescript-eslint/recommended',
     'plugin:@typescript-eslint/recommended-type-checked',

diff --git a/example/index-debug.html b/example/index-debug.html
@@ -0,0 +1,49 @@
+<html>
+  <head>
+    <script src="cram-bundle.js"></script>
+    <script>
+      const { IndexedCramFile, CramFile, CraiIndex } = window.gmodCRAM
+
+      // open local files
+      const indexedFile = new IndexedCramFile({
+        cramUrl: 'volvox-sorted.cram',
+        index: new CraiIndex({
+          url: 'volvox-sorted.cram.crai',
+        }),
+        seqFetch: async (seqId, start, end) => {
+          return ''
+        },
+        checkSequenceMD5: false,
+      })
+
+      // example of fetching records from an indexed CRAM file.
+      // NOTE: only numeric IDs for the reference sequence are accepted.
+      // For indexedfasta the numeric ID is the order in which the sequence names appear in the header
+
+      // Wrap in an async and then run
+      run = async () => {
+        const records = await indexedFile.getRecordsForRange(0, 10000, 20000)
+        const r = []
+        records.forEach(record => {
+          console.log(`got a record named ${record.readName}`)
+          if (record.readFeatures != undefined) {
+            record.readFeatures.forEach(({ code, pos, refPos, ref, sub }) => {
+              if (code === 'X') {
+                r.push(
+                  `${record.readName} shows a base substitution at ${refPos}`,
+                )
+              }
+            })
+          }
+        })
+        document.getElementById('output').innerHTML = r.join('\n')
+      }
+
+      run()
+    </script>
+  </head>
+  <body>
+    <h1>Hello world</h1>
+    <pre id="output" />
+  </body>
+</html>
diff --git a/src/cramFile/codecs/external.ts b/src/cramFile/codecs/external.ts
@@ -39,10 +39,6 @@ export default class ExternalCodec extends CramCodec<
     cursors: Cursors,
   ) {
     const { blockContentId } = this.parameters
-    // console.log({
-    //   blocksByContentId: Object.keys(blocksByContentId),
-    //   blockContentId,
-    // })
     const contentBlock = blocksByContentId[blockContentId]
     if (!contentBlock) {
       throw new CramMalformedError(

diff --git a/src/cramFile/slice/index.ts b/src/cramFile/slice/index.ts
@@ -198,7 +198,7 @@ export default class CramSlice {
     const sectionParsers = getSectionParsers(majorVersion)
     const containerHeader = await this.container.getHeader()
     if (!containerHeader) {
-      throw new Error('wow')
+      throw new Error('no container header detected')
     }
 
     const header = await this.file.readBlock(

diff --git a/webpack.config.js b/webpack.config.js
@@ -5,9 +5,6 @@ module.exports = {
   mode: 'production',
   entry: './dist/index.js',
   plugins: [
-    // this is needed to properly polyfill buffer in desktop, after the CRA5
-    // conversion it was observed cram, twobit, etc that use
-    // @gmod/binary-parser complained of buffers not being real buffers
     new webpack.ProvidePlugin({
       Buffer: ['buffer', 'Buffer'],
     }),