Optimizations for SNPCoverageAdapter (#5380)

Author: cmdcolin

eslint.config.mjs

@@ -22,7 +22,7 @@ export default defineConfig(
       'config/jest/*',
       'benchmarks/*',
       '**/build/**/*',
-      '**/dist/**/*',
+      '**/dist*/**/*',
       'scripts/analyze_cpuprof.ts',
       '**/esm/**/*',
       '**/public/**/*',

package.json

@@ -131,7 +131,6 @@
     "storybook": "^10.1.11",
     "style-loader": "^4.0.0",
     "terser-webpack-plugin": "^5.2.5",
-    "ts-node": "^10.4.0",
     "tslib": "^2.0.1",
     "typescript": "^5.8.0",
     "typescript-eslint": "^8.51.0",

packages/core/ui/EditableTypography.tsx

@@ -1,7 +1,7 @@
 import { forwardRef, useState } from 'react'
 
 import { makeStyles } from '@jbrowse/core/util/tss-react'
-import useMeasure from '../util/useMeasure'
+import useMeasure from '@jbrowse/core/util/useMeasure'
 import { InputBase, Typography, useTheme } from '@mui/material'
 
 import type { TypographyProps } from '@mui/material'

packages/core/util/index.ts

@@ -2,7 +2,7 @@ import type React from 'react'
 import { useEffect, useRef, useState } from 'react'
 
 import { unzip } from '@gmod/bgzf-filehandle'
-import useMeasure from './useMeasure'
+import useMeasure from '@jbrowse/core/util/useMeasure'
 import {
   getEnv as getEnvMST,
   getParent,

plugins/alignments/.gitignore

@@ -0,0 +1 @@
+dist_branch*

plugins/alignments/benches/pacbio_hg002.bam

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+set -e
+
+CURRENT_BRANCH=$(git branch --show-current)
+BRANCH1="${1:-main}"
+BRANCH2="${2:-$CURRENT_BRANCH}"
+
+if ! git diff --quiet || ! git diff --cached --quiet; then
+  echo "Error: Uncommitted changes detected. Please commit or stash your changes first."
+  exit 1
+fi
+
+rm -rf dist_branch1 dist_branch2
+
+echo "Building $BRANCH1 branch..."
+git checkout "$BRANCH1"
+yarn build
+mv dist dist_branch1
+echo "$BRANCH1" >dist_branch1/branchname.txt
+
+echo "Building $BRANCH2 branch..."
+git checkout "$BRANCH2"
+yarn build
+mv dist dist_branch2
+echo "$BRANCH2" >dist_branch2/branchname.txt
+
+echo "Build complete!"
+echo "$BRANCH1 build: dist_branch1/index.js"
+echo "$BRANCH2 build: dist_branch2/index.js"

plugins/alignments/benches/pacbio_hg002.bam.bai

@@ -141,12 +141,33 @@ export function forEachMismatchNumeric(
       soffset += len
       roffset += len
     } else if (op === CIGAR_I) {
-      let insertedBases = ''
-      for (let j = 0; j < len && soffset + j < seqLength; j++) {
-        const seqIdx = soffset + j
-        const sb = numericSeq[seqIdx >> 1]!
-        const nibble = (sb >> ((1 - (seqIdx & 1)) << 2)) & 0xf
-        insertedBases += SEQRET[nibble]!
+      // Optimized insertion base extraction - avoid string concat for common cases
+      const safeLen = Math.min(len, seqLength - soffset)
+      let insertedBases: string
+      if (safeLen === 1) {
+        // Single base insertion - most common case
+        const sb = numericSeq[soffset >> 1]!
+        const nibble = (sb >> ((1 - (soffset & 1)) << 2)) & 0xf
+        insertedBases = SEQRET[nibble]!
+      } else if (safeLen === 2) {
+        // Two base insertion - second most common
+        const seqIdx0 = soffset
+        const sb0 = numericSeq[seqIdx0 >> 1]!
+        const nibble0 = (sb0 >> ((1 - (seqIdx0 & 1)) << 2)) & 0xf
+        const seqIdx1 = soffset + 1
+        const sb1 = numericSeq[seqIdx1 >> 1]!
+        const nibble1 = (sb1 >> ((1 - (seqIdx1 & 1)) << 2)) & 0xf
+        insertedBases = SEQRET[nibble0]! + SEQRET[nibble1]!
+      } else {
+        // Longer insertions - use array join (avoids intermediate string allocations)
+        const bases = new Array<string>(safeLen)
+        for (let j = 0; j < safeLen; j++) {
+          const seqIdx = soffset + j
+          const sb = numericSeq[seqIdx >> 1]!
+          const nibble = (sb >> ((1 - (seqIdx & 1)) << 2)) & 0xf
+          bases[j] = SEQRET[nibble]!
+        }
+        insertedBases = bases.join('')
       }
       callback(INSERTION_TYPE, roffset, 0, insertedBases, -1, 0, len)
       soffset += len
@@ -198,6 +219,9 @@ export function forEachMismatchNumeric(
           } else if (mdMatchRemaining > 0) {
             mdMatchRemaining--
           }
+        } else if (ref) {
+          // No MD tag - get reference base from ref string
+          altbaseCode = ref.charCodeAt(roffset + j)
         }
 
         callback(

plugins/alignments/build.sh

@@ -5,7 +5,7 @@ const NUMERIC_CIGAR_CODES = [
   77, 73, 68, 78, 83, 72, 80, 61, 88, 63, 63, 63, 63, 63, 63, 63,
 ]
 
-function numericCigarToString(numeric: Uint32Array): string {
+function numericCigarToString(numeric: ArrayLike<number>): string {
   let result = ''
   for (let i = 0, l = numeric.length; i < l; i++) {
     const packed = numeric[i]!