add publish workflow with npm trusted publishing

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: cmdcolin

src/bgzfBlockScan.ts

@@ -20,8 +20,8 @@ export function scanBgzfBlocks(
 
   while (offset + BGZF_MIN_BLOCK_SIZE <= input.length) {
     if (
-      input[offset] !== 0x1f ||
-      input[offset + 1] !== 0x8b ||
+      input[offset] !== 0x1F ||
+      input[offset + 1] !== 0x8B ||
       input[offset + 2] !== 8 ||
       input[offset + 3] !== 4
     ) {

src/unzip.ts

@@ -6,20 +6,8 @@ import {
   decompressAll,
   decompressChunkSlice,
 } from './wasm/bgzf-wasm-inlined.js'
-import type { BgzfWorkerPool } from './workerPool.ts'
-
-export interface BlockCache {
-  get(key: string): { buffer: Uint8Array; bytesRead: number } | undefined
-  set(key: string, value: { buffer: Uint8Array; bytesRead: number }): void
-}
 
-export interface Filehandle {
-  read(
-    length: number,
-    position: number,
-    opts?: Record<string, unknown>,
-  ): Promise<Uint8Array>
-}
+import type { BgzfWorkerPool } from './workerPool.ts'
 
 interface VirtualOffset {
   blockPosition: number
@@ -31,7 +19,7 @@ interface Chunk {
 }
 
 function hasGzipHeader(data: Uint8Array) {
-  return data.length >= 2 && data[0] === 0x1f && data[1] === 0x8b
+  return data.length >= 2 && data[0] === 0x1F && data[1] === 0x8B
 }
 
 async function decompressGzip(inputData: Uint8Array) {

src/workerPool.ts

@@ -197,8 +197,6 @@ export async function createBgzfWorkerPool(
       const numW = workers.length
       const blocksPerWorker = Math.ceil(blocks.length / numW)
 
-      // Dispatch contiguous byte ranges — each worker calls decompressAll
-      // on its slice (single WASM call, single Decompressor, single output Vec)
       const rangeInfos: { startBlock: number; endBlock: number }[] = []
       const promises: Promise<RangeResult>[] = []
 

test/browser/index.html

@@ -36,7 +36,7 @@
         // Warmup
         for (let i = 0; i < 3; i++) {
           await unzipChunkSlice(data, chunk)
-          await unzipChunkSlice(data, chunk, undefined, pool)
+          await unzipChunkSlice(data, chunk, pool)
         }
 
         const seqStart = performance.now()
@@ -144,7 +144,7 @@
           ],
         ]) {
           const sequential = await unzipChunkSlice(data, chunk)
-          const parallel = await unzipChunkSlice(data, chunk, undefined, pool)
+          const parallel = await unzipChunkSlice(data, chunk, pool)
 
           const buffersMatch =
             sequential.buffer.length === parallel.buffer.length &&

test/workerPool.test.ts

@@ -41,6 +41,44 @@ test('scanBgzfBlocks on T_ko.2bit.gz', () => {
   expect(totalDecompressed).toBeGreaterThan(0)
 })
 
+test('scanBgzfBlocks returns empty for empty input', () => {
+  const blocks = scanBgzfBlocks(new Uint8Array(0), 0, 0)
+  expect(blocks).toEqual([])
+})
+
+test('scanBgzfBlocks returns empty for input shorter than min block size', () => {
+  const blocks = scanBgzfBlocks(new Uint8Array(25), 0, 100)
+  expect(blocks).toEqual([])
+})
+
+test('scanBgzfBlocks stops on truncated block', () => {
+  const testData = fs.readFileSync(require.resolve('./data/paired.bam'))
+  const allBlocks = scanBgzfBlocks(testData, 0, testData.length)
+  const firstBlockSize = allBlocks[0]!.compressedSize
+
+  // truncate in the middle of the second block
+  const truncated = testData.subarray(0, firstBlockSize + 10)
+  const blocks = scanBgzfBlocks(truncated, 0, truncated.length)
+  expect(blocks.length).toBe(1)
+  expect(blocks[0]!.compressedSize).toBe(firstBlockSize)
+})
+
+test('scanBgzfBlocks stops on non-bgzf data', () => {
+  const blocks = scanBgzfBlocks(new Uint8Array(1000), 0, 1000)
+  expect(blocks).toEqual([])
+})
+
+test('scanBgzfBlocks includes block at maxBlockPosition', () => {
+  const testData = fs.readFileSync(require.resolve('./data/paired.bam'))
+  const allBlocks = scanBgzfBlocks(testData, 0, testData.length)
+  // set maxBlockPosition to exactly the second block's position
+  const secondBlockPos = allBlocks[1]!.filePosition
+  const blocks = scanBgzfBlocks(testData, 0, secondBlockPos)
+  // should include the block at maxBlockPosition (inclusive)
+  expect(blocks.length).toBe(2)
+  expect(blocks[1]!.filePosition).toBe(secondBlockPos)
+})
+
 test('scanBgzfBlocks with large filePosition offset', () => {
   const testData = fs.readFileSync(require.resolve('./data/paired.bam'))
   const startPos = 5_000_000_000_000