@gmod/bam 7.6.0 → 7.6.2

package/dist/htsget.js

@@ -39,91 +39,111 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const bamFile_ts_1 = __importStar(require("./bamFile.js"));
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
-const sam_ts_1 = require("./sam.js");
 const util_ts_1 = require("./util.js");
 const virtualOffset_ts_1 = require("./virtualOffset.js");
-async function fetchOk(url, opts) {
-    const res = await fetch(url, opts);
+// Errors carry a JSON body naming the error type, e.g. {"htsget":
+// {"error":"InvalidAuthentication","message":"..."}}. Surface that rather than
+// the raw payload, since 401/403 are the first thing a misconfigured token hits.
+function htsgetErrorMessage(text) {
+    let parsed;
+    try {
+        parsed = JSON.parse(text);
+    }
+    catch {
+        // not JSON, fall through to the raw body
+    }
+    const err = parsed?.htsget;
+    return err?.error === undefined
+        ? text
+        : err.message === undefined
+            ? err.error
+            : `${err.error}: ${err.message}`;
+}
+/**
+ * Offset of the first alignment record in the concatenated ticket blocks.
+ *
+ * The spec has the client concatenate the blocks in ticket order to get a
+ * complete data stream, so whether the header is its own block is up to the
+ * server: htsnexus splits it into a leading `data:` url, while htsget-rs
+ * returns header and records together in a single url. Either way the
+ * concatenation starts with the BAM header, so seek past it rather than
+ * dropping blocks — a url count or class attribute can't tell the two layouts
+ * apart. Returns 0 when the stream has no header, which is what a server
+ * sending body-only blocks produces.
+ */
+function recordsOffset(uncba) {
+    const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
+    if (uncba.byteLength < 8 || dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
+        return 0;
+    }
+    const refs = (0, util_ts_1.parseRefSeqs)(uncba, 8 + dataView.getInt32(4, true), n => n);
+    if (!refs) {
+        throw new Error('truncated BAM header in htsget response');
+    }
+    return refs.end;
+}
+async function fetchOk(fetchFn, url, opts) {
+    const res = await fetchFn(url, opts);
     if (!res.ok) {
-        throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
+        throw new Error(`HTTP ${res.status} fetching ${url}: ${htsgetErrorMessage(await res.text())}`);
     }
     return res;
 }
-async function fetchChunk({ url, headers }, opts) {
+async function fetchChunk(fetchFn, { url, headers }, opts) {
     // pass base64 data URLs straight to fetch; otherwise apply headers (minus
     // referer, which isn't a permitted client-set header).
     // https://stackoverflow.com/a/54123275/2129219
     const { referer: _referer, ...rest } = headers ?? {};
     const res = url.startsWith('data:')
-        ? await fetchOk(url)
-        : await fetchOk(url, { ...opts, headers: rest });
+        ? await fetchOk(fetchFn, url)
+        : await fetchOk(fetchFn, url, { ...opts, headers: rest });
     return new Uint8Array(await res.arrayBuffer());
 }
-async function fetchAndConcat(arr, opts) {
+async function fetchAndConcat(fetchFn, arr, opts) {
     // Pipeline unzip after each fetch so decompression overlaps later fetches.
-    return (0, util_ts_1.concatUint8Array)(await Promise.all(arr.map(async (c) => (0, bgzf_filehandle_1.unzip)(await fetchChunk(c, opts)))));
+    return (0, util_ts_1.concatUint8Array)(await Promise.all(arr.map(async (c) => (0, bgzf_filehandle_1.unzip)(await fetchChunk(fetchFn, c, opts)))));
 }
 class HtsgetFile extends bamFile_ts_1.default {
     baseUrl;
     trackId;
+    fetchFn;
     constructor(args) {
         super({ htsget: true, recordClass: args.recordClass });
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
+        this.fetchFn = args.fetch ?? ((input, init) => fetch(input, init));
+    }
+    /**
+     * Requests a ticket and returns its data blocks decompressed and
+     * concatenated, which per the spec is a complete BAM stream.
+     */
+    async fetchTicket(query, opts) {
+        const url = `${this.baseUrl}/${this.trackId}?${query}`;
+        const res = await fetchOk(this.fetchFn, url, { signal: opts?.signal });
+        const ticket = await res.json();
+        return fetchAndConcat(this.fetchFn, ticket.htsget.urls, {
+            signal: opts?.signal,
+        });
     }
     async getRecordsForRange(chr, min, max, opts) {
         await this.getHeader(opts);
-        const base = `${this.baseUrl}/${this.trackId}`;
-        const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
         const chrId = this.chrToIndex?.[chr];
         if (chrId === undefined) {
             return [];
         }
-        const result = await fetchOk(url, opts);
-        const data = await result.json();
-        const uncba = await fetchAndConcat(data.htsget.urls.slice(1), {
-            signal: opts?.signal,
-        });
+        const uncba = await this.fetchTicket(`referenceName=${chr}&start=${min}&end=${max}&format=BAM`, opts);
         const zero = new virtualOffset_ts_1.VirtualOffset(0, 0);
-        const allRecords = this.readBamFeatures(uncba, [], [], new chunk_ts_1.default(zero, zero, 0));
-        return (0, util_ts_1.appendInRange)(allRecords, chrId, min, max);
+        const records = this.readBamFeatures(uncba.subarray(recordsOffset(uncba)), [], [], new chunk_ts_1.default(zero, zero, 0));
+        return (0, util_ts_1.appendInRange)(records, chrId, min, max);
     }
     async getHeaderPre(opts = {}) {
-        const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
-        const result = await fetchOk(url, opts);
-        const data = await result.json();
-        const uncba = await fetchAndConcat(data.htsget.urls, {
-            signal: opts.signal,
-        });
-        const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
-        if (dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
-            throw new Error('Not a BAM file');
-        }
-        const headLen = dataView.getInt32(4, true);
-        const decoder = new TextDecoder();
-        const headerText = decoder.decode(uncba.subarray(8, 8 + headLen));
-        const samHeader = (0, sam_ts_1.parseHeaderText)(headerText);
-        // use the @SQ lines in the header to figure out the
-        // mapping between ref ref ID numbers and names
-        const idToName = [];
-        const nameToId = {};
-        const sqLines = samHeader.filter(l => l.tag === 'SQ');
-        for (const [refId, sqLine] of sqLines.entries()) {
-            let refName = '';
-            let length = 0;
-            for (const item of sqLine.data) {
-                if (item.tag === 'SN') {
-                    refName = item.value;
-                }
-                else if (item.tag === 'LN') {
-                    length = +item.value;
-                }
-            }
-            nameToId[refName] = refId;
-            idToName[refId] = { refName, length };
+        // format is the only parameter the spec permits alongside class=header;
+        // servers SHOULD reject anything else with InvalidInput
+        const uncba = await this.fetchTicket('class=header&format=BAM', opts);
+        const samHeader = this.applyHeader(uncba);
+        if (!samHeader) {
+            throw new Error('Insufficient data for reference sequences');
         }
-        this.chrToIndex = nameToId;
-        this.indexToChr = idToName;
         return samHeader;
     }
 }

package/dist/htsget.js.map

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package/dist/index.d.ts

@@ -5,3 +5,4 @@ export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';
 export type { Bytes } from './record.ts';
 export type { BamRecordClass, BamRecordLike } from './bamFile.ts';
+export type { Fetcher } from 'generic-filehandle2';

package/dist/util.d.ts

@@ -1,5 +1,6 @@
 import Chunk from './chunk.ts';
-import type { Offset, VirtualOffset } from './virtualOffset.ts';
+import { VirtualOffset } from './virtualOffset.ts';
+import type { Offset } from './virtualOffset.ts';
 export interface BamOpts {
     viewAsPairs?: boolean;
     pairAcrossChr?: boolean;
@@ -35,8 +36,24 @@ export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRef
         refName: string;
         length: number;
     }[];
+    end: number;
 } | undefined;
-export declare function findFirstData(firstDataLine: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
+/**
+ * The smallest of `current` and the `count` packed virtual offsets starting at
+ * `offset`, allocating at most one VirtualOffset rather than one per entry.
+ *
+ * 0:0 is skipped rather than treated as the minimum. No BAM record can live
+ * there — the magic and header occupy the start of the file — so it is the
+ * "unset" placeholder htslib leaves in linear-index windows ahead of a
+ * reference's first read (see test/data/HG00096_illumina_lowcov.bam.bai, whose
+ * first three windows are 0). Counting it collapses firstDataLine to 0:0 and
+ * makes callers size a header read from nothing.
+ *
+ * The index first pass exists only to find this minimum, and it visits every
+ * linear-index entry in the file to do it. Building a VirtualOffset per entry
+ * to compare and discard it is the bulk of that pass.
+ */
+export declare function minVirtualOffset(bytes: Uint8Array, offset: number, count: number, current: VirtualOffset | undefined): VirtualOffset | undefined;
 export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (arg: string) => string): {
     refNameToId: Record<string, number>;
     refIdToName: string[];

package/dist/util.js

@@ -7,12 +7,13 @@ exports.optimizeChunks = optimizeChunks;
 exports.parsePseudoBin = parsePseudoBin;
 exports.clampChunkEnds = clampChunkEnds;
 exports.parseRefSeqs = parseRefSeqs;
-exports.findFirstData = findFirstData;
+exports.minVirtualOffset = minVirtualOffset;
 exports.parseNameBytes = parseNameBytes;
 exports.concatUint8Array = concatUint8Array;
 exports.appendInRange = appendInRange;
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
 const long_ts_1 = require("./long.js");
+const virtualOffset_ts_1 = require("./virtualOffset.js");
 function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
     if (n === 0) {
@@ -138,14 +139,48 @@ function parseRefSeqs(uncba, start, renameRefSeq) {
         indexToChr.push({ refName, length: lRef });
         p += 8 + lName;
     }
-    return { chrToIndex, indexToChr };
+    // end is the offset just past the header, i.e. where alignment records start
+    return { chrToIndex, indexToChr, end: p };
 }
-function findFirstData(firstDataLine, virtualOffset) {
-    return firstDataLine
-        ? firstDataLine.compareTo(virtualOffset) > 0
-            ? virtualOffset
-            : firstDataLine
-        : virtualOffset;
+// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset — but NOT the 0:0
+// skip below, which is only sound for BAM. A tabix'd file with no header lines
+// really does have its first record at 0:0.
+/**
+ * The smallest of `current` and the `count` packed virtual offsets starting at
+ * `offset`, allocating at most one VirtualOffset rather than one per entry.
+ *
+ * 0:0 is skipped rather than treated as the minimum. No BAM record can live
+ * there — the magic and header occupy the start of the file — so it is the
+ * "unset" placeholder htslib leaves in linear-index windows ahead of a
+ * reference's first read (see test/data/HG00096_illumina_lowcov.bam.bai, whose
+ * first three windows are 0). Counting it collapses firstDataLine to 0:0 and
+ * makes callers size a header read from nothing.
+ *
+ * The index first pass exists only to find this minimum, and it visits every
+ * linear-index entry in the file to do it. Building a VirtualOffset per entry
+ * to compare and discard it is the bulk of that pass.
+ */
+function minVirtualOffset(bytes, offset, count, current) {
+    let minBlock = current ? current.blockPosition : Infinity;
+    let minData = current ? current.dataPosition : 0;
+    let found = false;
+    for (let i = 0; i < count; i++) {
+        const p = offset + i * 8;
+        const block = bytes[p + 7] * 0x10000000000 +
+            bytes[p + 6] * 0x100000000 +
+            bytes[p + 5] * 0x1000000 +
+            bytes[p + 4] * 0x10000 +
+            bytes[p + 3] * 0x100 +
+            bytes[p + 2];
+        const data = (bytes[p + 1] << 8) | bytes[p];
+        if ((block !== 0 || data !== 0) &&
+            (block < minBlock || (block === minBlock && data < minData))) {
+            minBlock = block;
+            minData = data;
+            found = true;
+        }
+    }
+    return found ? new virtualOffset_ts_1.VirtualOffset(minBlock, minData) : current;
 }
 // SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
 function parseNameBytes(namesBytes, renameRefSeq = s => s) {

package/dist/util.js.map

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package/esm/bai.js

@@ -1,6 +1,6 @@
 import Chunk from "./chunk.js";
 import IndexFile, { memoizeByRefId } from "./indexFile.js";
-import { clampChunkEnds, findFirstData, parsePseudoBin } from "./util.js";
+import { clampChunkEnds, minVirtualOffset, parsePseudoBin } from "./util.js";
 import { fromBytes } from "./virtualOffset.js";
 const BAI_MAGIC = 21578050; // BAI\1
 // BAI uses a fixed 5-level binning scheme with a 14-bit (16KB) linear index
@@ -69,10 +69,8 @@ export default class BAI extends IndexFile {
             // marks where the BAM header ends and data begins
             const linearCount = dataView.getInt32(curr, true);
             curr += 4;
-            for (let j = 0; j < linearCount; j++) {
-                firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr));
-                curr += 8;
-            }
+            firstDataLine = minVirtualOffset(bytes, curr, linearCount, firstDataLine);
+            curr += 8 * linearCount;
         }
         function getIndices(refId) {
             let curr = offsets[refId];

package/esm/bai.js.map

@@ -1 +1 @@
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package/esm/bamFile.d.ts

@@ -73,6 +73,19 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
             value: string;
         }[];
     }[] | undefined>;
+    /**
+     * Installs the header text and ref name/id maps from the start of a
+     * decompressed BAM stream, returning the parsed SAM header lines. Returns
+     * undefined if the stream is cut off partway through the ref-seq table, so
+     * the caller can retry with more data.
+     */
+    protected applyHeader(uncba: Uint8Array): {
+        tag: string;
+        data: {
+            tag: string;
+            value: string;
+        }[];
+    }[] | undefined;
     getHeader(opts?: BaseOpts): Promise<{
         tag: string;
         data: {

package/esm/bamFile.js

@@ -9,6 +9,11 @@ import { parseHeaderText } from "./sam.js";
 import { appendInRange, parseRefSeqs } from "./util.js";
 export const BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
+// Ceiling on the header read. A million contigs is roughly 10MB of compressed
+// @SQ lines and ref-seq table, so anything past this is a corrupt header
+// claiming a huge n_ref rather than a real one, and growing the read further
+// just downloads the file.
+const maxHeaderReadLen = 32 * 1024 * 1024;
 function resolveFilehandle(filehandle, path, url) {
     return (filehandle ??
         (path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined));
@@ -128,37 +133,52 @@ export default class BamFile {
             return undefined;
         }
         const indexData = await this.index.parse(opts);
-        // firstDataLine is not defined in cases where there is no data in the file
-        // (just bam header and nothing else)
-        const readLen = indexData.firstDataLine === undefined
-            ? undefined
+        // The records start at firstDataLine, so reading up to it plus the bgzf
+        // block straddling it covers the header. It is undefined when the index
+        // records no data at all (header-only BAM), and it undershoots when the
+        // index leaves offsets unset, so grow the read until the ref-seq table
+        // parses. Never readFile() here: on a remote BAM that is a whole-file
+        // download to read a header.
+        let readLen = indexData.firstDataLine === undefined
+            ? blockLen
             : indexData.firstDataLine.blockPosition + blockLen;
-        const buffer = readLen === undefined
-            ? await this.bam.readFile()
-            : await this.bam.read(readLen, 0);
-        let uncba = await unzip(buffer);
+        let samHeader;
+        let atEof = false;
+        while (samHeader === undefined && !atEof && readLen <= maxHeaderReadLen) {
+            const buffer = await this.bam.read(readLen, 0, { signal: opts.signal });
+            // a short read means readLen ran past the end of the file, so there are
+            // no more bytes to grow into
+            atEof = buffer.length < readLen;
+            samHeader = this.applyHeader(await unzip(buffer));
+            readLen *= 2;
+        }
+        if (samHeader === undefined) {
+            throw new Error('Insufficient data for reference sequences');
+        }
+        return samHeader;
+    }
+    /**
+     * Installs the header text and ref name/id maps from the start of a
+     * decompressed BAM stream, returning the parsed SAM header lines. Returns
+     * undefined if the stream is cut off partway through the ref-seq table, so
+     * the caller can retry with more data.
+     */
+    applyHeader(uncba) {
         const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
         if (dataView.getInt32(0, true) !== BAM_MAGIC) {
             throw new Error('Not a BAM file');
         }
         const headLen = dataView.getInt32(4, true);
-        this.header = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
-        // BAM files with many reference sequences may need more data than the
-        // initial read covers. If the first attempt comes up short, fall back to
-        // reading the whole file (the index's firstDataLine is just an
-        // optimization hint, not a guaranteed cap on the ref-seq table size).
-        const refSeqStart = headLen + 8;
-        let parsed = parseRefSeqs(uncba, refSeqStart, this.renameRefSeq);
-        if (!parsed) {
-            uncba = await unzip(await this.bam.readFile());
-            parsed = parseRefSeqs(uncba, refSeqStart, this.renameRefSeq);
-        }
-        if (!parsed) {
-            throw new Error('Insufficient data for reference sequences');
+        const parsed = parseRefSeqs(uncba, headLen + 8, this.renameRefSeq);
+        let samHeader;
+        if (parsed) {
+            const headerText = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
+            this.header = headerText;
+            this.chrToIndex = parsed.chrToIndex;
+            this.indexToChr = parsed.indexToChr;
+            samHeader = parseHeaderText(headerText);
         }
-        this.chrToIndex = parsed.chrToIndex;
-        this.indexToChr = parsed.indexToChr;
-        return parseHeaderText(this.header);
+        return samHeader;
     }
     getHeader(opts) {
         if (!this.headerP) {

package/esm/bamFile.js.map

@@ -1 +1 @@
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package/esm/csi.js

@@ -1,7 +1,7 @@
 import { unzip } from '@gmod/bgzf-filehandle';
 import Chunk from "./chunk.js";
 import IndexFile, { memoizeByRefId } from "./indexFile.js";
-import { clampChunkEnds, findFirstData, parseNameBytes, parsePseudoBin, } from "./util.js";
+import { clampChunkEnds, minVirtualOffset, parseNameBytes, parsePseudoBin, } from "./util.js";
 import { VirtualOffset, fromBytes } from "./virtualOffset.js";
 const CSI1_MAGIC = 21582659; // CSI\1
 const CSI2_MAGIC = 38359875; // CSI\2
@@ -89,15 +89,14 @@ export default class CSI extends IndexFile {
                     curr += 28 + 16;
                 }
                 else {
-                    curr += 8;
+                    // A bin's loffset is the smallest virtual offset of any record in it,
+                    // so the minimum over loffsets is already the minimum over the bin's
+                    // chunks — one read per bin instead of one per chunk. Checked against
+                    // every .csi in test/data: same answer on all 19.
+                    firstDataLine = minVirtualOffset(bytes, curr, 1, firstDataLine);
+                    curr += 8; // loffset
                     const chunkCount = dataView.getInt32(curr, true);
-                    curr += 4;
-                    for (let k = 0; k < chunkCount; k += 1) {
-                        const u = fromBytes(bytes, curr);
-                        curr += 8;
-                        curr += 8;
-                        firstDataLine = findFirstData(firstDataLine, u);
-                    }
+                    curr += 4 + 16 * chunkCount;
                 }
             }
         }