@gmod/bam 8.11.1 → 9.0.1

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Files changed (14) hide show
  1. package/README.md +6 -4
  2. package/dist/htsget.d.ts +7 -6
  3. package/dist/htsget.js +21 -10
  4. package/dist/htsget.js.map +1 -1
  5. package/dist/record.js +6 -1
  6. package/dist/record.js.map +1 -1
  7. package/esm/htsget.d.ts +7 -6
  8. package/esm/htsget.js +21 -10
  9. package/esm/htsget.js.map +1 -1
  10. package/esm/record.js +6 -1
  11. package/esm/record.js.map +1 -1
  12. package/package.json +1 -1
  13. package/src/htsget.ts +28 -26
  14. package/src/record.ts +6 -1
package/README.md CHANGED
@@ -36,10 +36,12 @@ const bam = new BamFile({
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  Over HTTP it is worth putting
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  [`@gmod/range-cache-filehandle`](https://github.com/GMOD/range-cache-filehandle)
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- underneath the filehandle. It caches what it reads in 256 KiB chunks and turns
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- the chunks a read is missing into one request per contiguous run, so the
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- scattered index and data reads a query makes arrive as a couple of fetches
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- rather than dozens. `bamFilehandle` and `baiFilehandle` accept any
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+ underneath the filehandle. A query fetches the index once, then reads the
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+ records as a handful of byte ranges spread through the BAM —
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+ [this visualizer](https://cmdcolin.github.io/bam_index_visualizer) draws that
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+ pattern for a file of your choosing. The cache serves those ranges out of 256
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+ KiB chunks, so neighboring ranges share a request and later queries reuse what
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+ is already fetched. `bamFilehandle` and `baiFilehandle` accept any
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  generic-filehandle2 object, so it drops straight in:
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  ```typescript
package/dist/htsget.d.ts CHANGED
@@ -12,12 +12,13 @@ export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends Bam
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  baseUrl: string;
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  recordClass?: BamRecordClass<T>;
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  /**
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- * fetch implementation used for every request, so an `Authorization: Bearer
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- * <token>` header can be added for servers that require one. It is also
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- * called with the data-block urls from the ticket, which may point at
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- * third-party hosts, so only attach credentials to hosts you trust — the
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- * spec has servers put whatever a data block needs in that url's own
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- * `headers` field, which is applied either way.
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+ * fetch implementation for the **ticket request**, so an `Authorization:
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+ * Bearer <token>` header can be added for endpoints that require one.
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+ *
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+ * The data blocks a ticket names are NOT fetched with it — they can point
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+ * at any host, and the spec forbids sending the API's token to them. A
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+ * block needing authorization carries it in the ticket's own `headers`
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+ * field for that url, which is applied regardless.
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  */
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  fetch?: Fetcher;
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  /**
package/dist/htsget.js CHANGED
@@ -56,19 +56,28 @@ async function fetchOk(fetchFn, url, opts) {
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  }
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  return res;
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  }
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- async function fetchChunk(fetchFn, { url, headers }, opts) {
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+ /**
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+ * Data blocks are fetched with the global fetch, never with the ticket fetcher.
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+ * The spec is explicit ("HTTPS data block URLs", rule 6): a block url must
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+ * carry whatever credential it needs itself, in the url or in its own `headers`,
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+ * and the client "must not send the bearer token used for the API, if any, to
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+ * the data block endpoint, unless copied in the required `headers`". A ticket
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+ * can name any host, so honouring that is the difference between one endpoint's
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+ * token going to that endpoint and it going wherever a ticket points.
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+ */
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+ async function fetchChunk({ url, headers }, opts) {
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  // pass base64 data URLs straight to fetch; otherwise apply headers (minus
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  // referer, which isn't a permitted client-set header).
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  // https://stackoverflow.com/a/54123275/2129219
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  const { referer: _referer, ...rest } = headers ?? {};
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  const res = url.startsWith('data:')
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- ? await fetchOk(fetchFn, url)
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- : await fetchOk(fetchFn, url, { ...opts, headers: rest });
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+ ? await fetchOk(fetch, url)
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+ : await fetchOk(fetch, url, { ...opts, headers: rest });
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  return new Uint8Array(await res.arrayBuffer());
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  }
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- async function fetchAndConcat(fetchFn, arr, opts) {
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+ async function fetchAndConcat(arr, opts) {
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  // Pipeline unzip after each fetch so decompression overlaps later fetches.
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- return (0, util_ts_1.concatUint8Array)(await Promise.all(arr.map(async (c) => (0, bgzf_filehandle_1.unzip)(await fetchChunk(fetchFn, c, opts)))));
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+ return (0, util_ts_1.concatUint8Array)(await Promise.all(arr.map(async (c) => (0, bgzf_filehandle_1.unzip)(await fetchChunk(c, opts)))));
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  }
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  class HtsgetFile extends bamFile_ts_1.default {
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  baseUrl;
@@ -91,12 +100,14 @@ class HtsgetFile extends bamFile_ts_1.default {
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  * concatenated, which per the spec is a complete BAM stream.
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  */
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  async fetchTicket(query, opts) {
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- const url = `${this.baseUrl}/${this.trackId}?${query}`;
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+ // Exactly one slash between the two. An id may contain "/" and the spec's
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+ // own examples start with one ("/byStudy/PRJEB4019"), while an endpoint is
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+ // as often written with a trailing slash as without; concatenating raw
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+ // produced "//" for either.
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+ const url = `${this.baseUrl.replace(/\/+$/, '')}/${this.trackId.replace(/^\/+/, '')}?${query}`;
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  const res = await fetchOk(this.fetchFn, url, { signal: opts?.signal });
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  const ticket = await res.json();
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- return fetchAndConcat(this.fetchFn, ticket.htsget.urls, {
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- signal: opts?.signal,
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- });
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+ return fetchAndConcat(ticket.htsget.urls, { signal: opts?.signal });
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  }
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  async getRecordsForRange(chr, min, max, opts) {
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  await this.getHeader(opts);
@@ -104,7 +115,7 @@ class HtsgetFile extends bamFile_ts_1.default {
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  if (chrId === undefined) {
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  return [];
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  }
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- const uncba = await this.fetchTicket(`referenceName=${chr}&start=${min}&end=${max}&format=BAM`, opts);
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+ const uncba = await this.fetchTicket(`referenceName=${encodeURIComponent(chr)}&start=${min}&end=${max}&format=BAM`, opts);
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  const zero = new virtualOffset_ts_1.VirtualOffset(0, 0);
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  const records = this.readBamFeatures(uncba.subarray(recordsOffset(uncba)), [], [], new chunk_ts_1.default(zero, zero, 0));
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  const result = (0, util_ts_1.appendInRange)(records, chrId, min, max);
package/dist/htsget.js.map CHANGED
@@ -1 +1 @@
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1
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package/dist/record.js CHANGED
@@ -354,9 +354,14 @@ class BamRecord {
354
354
  get start() {
355
355
  return this._dataView.getInt32(this._start + 8, true);
356
356
  }
357
+ // The end htslib's bam_endpos() reports: a record consuming no reference —
358
+ // an unmapped mate placed at its mate's coordinate, or an empty CIGAR —
359
+ // still covers one base rather than none, so a consumer's interval search on
360
+ // the base it sits at can find it (endpos() in util.ts applies the same rule
361
+ // to this library's own range filter).
357
362
  get end() {
358
363
  if (this._cachedEnd === undefined) {
359
- this._cachedEnd = this.start + this.length_on_ref;
364
+ this._cachedEnd = this.start + Math.max(this.length_on_ref, 1);
360
365
  }
361
366
  return this._cachedEnd;
362
367
  }
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/htsget.d.ts CHANGED
@@ -12,12 +12,13 @@ export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends Bam
12
12
  baseUrl: string;
13
13
  recordClass?: BamRecordClass<T>;
14
14
  /**
15
- * fetch implementation used for every request, so an `Authorization: Bearer
16
- * <token>` header can be added for servers that require one. It is also
17
- * called with the data-block urls from the ticket, which may point at
18
- * third-party hosts, so only attach credentials to hosts you trust — the
19
- * spec has servers put whatever a data block needs in that url's own
20
- * `headers` field, which is applied either way.
15
+ * fetch implementation for the **ticket request**, so an `Authorization:
16
+ * Bearer <token>` header can be added for endpoints that require one.
17
+ *
18
+ * The data blocks a ticket names are NOT fetched with it — they can point
19
+ * at any host, and the spec forbids sending the API's token to them. A
20
+ * block needing authorization carries it in the ticket's own `headers`
21
+ * field for that url, which is applied regardless.
21
22
  */
22
23
  fetch?: Fetcher;
23
24
  /**
package/esm/htsget.js CHANGED
@@ -51,19 +51,28 @@ async function fetchOk(fetchFn, url, opts) {
51
51
  }
52
52
  return res;
53
53
  }
54
- async function fetchChunk(fetchFn, { url, headers }, opts) {
54
+ /**
55
+ * Data blocks are fetched with the global fetch, never with the ticket fetcher.
56
+ * The spec is explicit ("HTTPS data block URLs", rule 6): a block url must
57
+ * carry whatever credential it needs itself, in the url or in its own `headers`,
58
+ * and the client "must not send the bearer token used for the API, if any, to
59
+ * the data block endpoint, unless copied in the required `headers`". A ticket
60
+ * can name any host, so honouring that is the difference between one endpoint's
61
+ * token going to that endpoint and it going wherever a ticket points.
62
+ */
63
+ async function fetchChunk({ url, headers }, opts) {
55
64
  // pass base64 data URLs straight to fetch; otherwise apply headers (minus
56
65
  // referer, which isn't a permitted client-set header).
57
66
  // https://stackoverflow.com/a/54123275/2129219
58
67
  const { referer: _referer, ...rest } = headers ?? {};
59
68
  const res = url.startsWith('data:')
60
- ? await fetchOk(fetchFn, url)
61
- : await fetchOk(fetchFn, url, { ...opts, headers: rest });
69
+ ? await fetchOk(fetch, url)
70
+ : await fetchOk(fetch, url, { ...opts, headers: rest });
62
71
  return new Uint8Array(await res.arrayBuffer());
63
72
  }
64
- async function fetchAndConcat(fetchFn, arr, opts) {
73
+ async function fetchAndConcat(arr, opts) {
65
74
  // Pipeline unzip after each fetch so decompression overlaps later fetches.
66
- return concatUint8Array(await Promise.all(arr.map(async (c) => unzip(await fetchChunk(fetchFn, c, opts)))));
75
+ return concatUint8Array(await Promise.all(arr.map(async (c) => unzip(await fetchChunk(c, opts)))));
67
76
  }
68
77
  export default class HtsgetFile extends BamFile {
69
78
  baseUrl;
@@ -86,12 +95,14 @@ export default class HtsgetFile extends BamFile {
86
95
  * concatenated, which per the spec is a complete BAM stream.
87
96
  */
88
97
  async fetchTicket(query, opts) {
89
- const url = `${this.baseUrl}/${this.trackId}?${query}`;
98
+ // Exactly one slash between the two. An id may contain "/" and the spec's
99
+ // own examples start with one ("/byStudy/PRJEB4019"), while an endpoint is
100
+ // as often written with a trailing slash as without; concatenating raw
101
+ // produced "//" for either.
102
+ const url = `${this.baseUrl.replace(/\/+$/, '')}/${this.trackId.replace(/^\/+/, '')}?${query}`;
90
103
  const res = await fetchOk(this.fetchFn, url, { signal: opts?.signal });
91
104
  const ticket = await res.json();
92
- return fetchAndConcat(this.fetchFn, ticket.htsget.urls, {
93
- signal: opts?.signal,
94
- });
105
+ return fetchAndConcat(ticket.htsget.urls, { signal: opts?.signal });
95
106
  }
96
107
  async getRecordsForRange(chr, min, max, opts) {
97
108
  await this.getHeader(opts);
@@ -99,7 +110,7 @@ export default class HtsgetFile extends BamFile {
99
110
  if (chrId === undefined) {
100
111
  return [];
101
112
  }
102
- const uncba = await this.fetchTicket(`referenceName=${chr}&start=${min}&end=${max}&format=BAM`, opts);
113
+ const uncba = await this.fetchTicket(`referenceName=${encodeURIComponent(chr)}&start=${min}&end=${max}&format=BAM`, opts);
103
114
  const zero = new VirtualOffset(0, 0);
104
115
  const records = this.readBamFeatures(uncba.subarray(recordsOffset(uncba)), [], [], new Chunk(zero, zero, 0));
105
116
  const result = appendInRange(records, chrId, min, max);
package/esm/htsget.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EACL,SAAS,EACT,aAAa,EACb,gBAAgB,EAChB,YAAY,GACb,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AA2BlD,kEAAkE;AAClE,+EAA+E;AAC/E,iFAAiF;AACjF,SAAS,kBAAkB,CAAC,IAAY;IACtC,IAAI,MAAmC,CAAA;IACvC,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IAAC,MAAM,CAAC;QACP,yCAAyC;IAC3C,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,EAAE,MAAM,CAAA;IAC1B,OAAO,GAAG,EAAE,KAAK,KAAK,SAAS;QAC7B,CAAC,CAAC,IAAI;QACN,CAAC,CAAC,GAAG,CAAC,OAAO,KAAK,SAAS;YACzB,CAAC,CAAC,GAAG,CAAC,KAAK;YACX,CAAC,CAAC,GAAG,GAAG,CAAC,KAAK,KAAK,GAAG,CAAC,OAAO,EAAE,CAAA;AACtC,CAAC;AAED;;;;;;;;;;;GAWG;AACH,SAAS,aAAa,CAAC,KAAiB;IACtC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;QACrE,OAAO,CAAC,CAAA;IACV,CAAC;IACD,MAAM,IAAI,GAAG,YAAY,CAAC,KAAK,EAAE,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxE,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,yCAAyC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,IAAI,CAAC,GAAG,CAAA;AACjB,CAAC;AAED,KAAK,UAAU,OAAO,CAAC,OAAgB,EAAE,GAAW,EAAE,IAAkB;IACtE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACpC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,kBAAkB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,EAAE,CAC9E,CAAA;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED;;;;;;;;GAQG;AACH,KAAK,UAAU,UAAU,CAAC,EAAE,GAAG,EAAE,OAAO,EAAe,EAAE,IAAkB;IACzE,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC;QAC3B,CAAC,CAAC,MAAM,OAAO,CAAC,KAAK,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IACzD,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAAC,GAAkB,EAAE,IAAkB;IAClE,2EAA2E;IAC3E,OAAO,gBAAgB,CACrB,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,KAAK,CAAC,MAAM,UAAU,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CACxE,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAEnB,SAAQ,OAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEf,OAAO,CAAS;IAExB,YAAY,IAkCX;QACC,KAAK,CAAC;YACJ,MAAM,EAAE,IAAI;YACZ,WAAW,EAAE,IAAI,CAAC,WAAW;YAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;YACjC,kBAAkB,EAAE,IAAI,CAAC,kBAAkB;YAC3C,sBAAsB,EAAE,IAAI,CAAC,sBAAsB;SACpD,CAAC,CAAA;QACF,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;IACpE,CAAC;IAED;;;OAGG;IACK,KAAK,CAAC,WAAW,CAAC,KAAa,EAAE,IAAe;QACtD,0EAA0E;QAC1E,2EAA2E;QAC3E,uEAAuE;QACvE,4BAA4B;QAC5B,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,IAAI,KAAK,EAAE,CAAA;QAC9F,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;QACtE,MAAM,MAAM,GAAiB,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;QAC7C,OAAO,cAAc,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;IACrE,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAClC,iBAAiB,kBAAkB,CAAC,GAAG,CAAC,UAAU,GAAG,QAAQ,GAAG,aAAa,EAC7E,IAAI,CACL,CAAA;QACD,MAAM,IAAI,GAAG,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,OAAO,GAAG,IAAI,CAAC,eAAe,CAClC,KAAK,CAAC,QAAQ,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EACpC,EAAE,EACF,EAAE,EACF,IAAI,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QACD,MAAM,MAAM,GAAG,aAAa,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;QACtD,MAAM,IAAI,CAAC,uBAAuB,CAAC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;QAC5D,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,wEAAwE;QACxE,wDAAwD;QACxD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,yBAAyB,EAAE,IAAI,CAAC,CAAA;QACrE,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QACzC,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAA;QAC9D,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}
package/esm/record.js CHANGED
@@ -349,9 +349,14 @@ export default class BamRecord {
349
349
  get start() {
350
350
  return this._dataView.getInt32(this._start + 8, true);
351
351
  }
352
+ // The end htslib's bam_endpos() reports: a record consuming no reference —
353
+ // an unmapped mate placed at its mate's coordinate, or an empty CIGAR —
354
+ // still covers one base rather than none, so a consumer's interval search on
355
+ // the base it sits at can find it (endpos() in util.ts applies the same rule
356
+ // to this library's own range filter).
352
357
  get end() {
353
358
  if (this._cachedEnd === undefined) {
354
- this._cachedEnd = this.start + this.length_on_ref;
359
+ this._cachedEnd = this.start + Math.max(this.length_on_ref, 1);
355
360
  }
356
361
  return this._cachedEnd;
357
362
  }
package/esm/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "8.11.1",
3
+ "version": "9.0.1",
4
4
  "packageManager": "pnpm@11.15.1",
5
5
  "description": "Parser for BAM and BAM index (bai) files",
6
6
  "license": "MIT",
package/src/htsget.ts CHANGED
@@ -91,31 +91,30 @@ async function fetchOk(fetchFn: Fetcher, url: string, opts?: RequestInit) {
91
91
  return res
92
92
  }
93
93
 
94
- async function fetchChunk(
95
- fetchFn: Fetcher,
96
- { url, headers }: HtsgetChunk,
97
- opts?: RequestInit,
98
- ) {
94
+ /**
95
+ * Data blocks are fetched with the global fetch, never with the ticket fetcher.
96
+ * The spec is explicit ("HTTPS data block URLs", rule 6): a block url must
97
+ * carry whatever credential it needs itself, in the url or in its own `headers`,
98
+ * and the client "must not send the bearer token used for the API, if any, to
99
+ * the data block endpoint, unless copied in the required `headers`". A ticket
100
+ * can name any host, so honouring that is the difference between one endpoint's
101
+ * token going to that endpoint and it going wherever a ticket points.
102
+ */
103
+ async function fetchChunk({ url, headers }: HtsgetChunk, opts?: RequestInit) {
99
104
  // pass base64 data URLs straight to fetch; otherwise apply headers (minus
100
105
  // referer, which isn't a permitted client-set header).
101
106
  // https://stackoverflow.com/a/54123275/2129219
102
107
  const { referer: _referer, ...rest } = headers ?? {}
103
108
  const res = url.startsWith('data:')
104
- ? await fetchOk(fetchFn, url)
105
- : await fetchOk(fetchFn, url, { ...opts, headers: rest })
109
+ ? await fetchOk(fetch, url)
110
+ : await fetchOk(fetch, url, { ...opts, headers: rest })
106
111
  return new Uint8Array(await res.arrayBuffer())
107
112
  }
108
113
 
109
- async function fetchAndConcat(
110
- fetchFn: Fetcher,
111
- arr: HtsgetChunk[],
112
- opts?: RequestInit,
113
- ) {
114
+ async function fetchAndConcat(arr: HtsgetChunk[], opts?: RequestInit) {
114
115
  // Pipeline unzip after each fetch so decompression overlaps later fetches.
115
116
  return concatUint8Array(
116
- await Promise.all(
117
- arr.map(async c => unzip(await fetchChunk(fetchFn, c, opts))),
118
- ),
117
+ await Promise.all(arr.map(async c => unzip(await fetchChunk(c, opts)))),
119
118
  )
120
119
  }
121
120
 
@@ -133,12 +132,13 @@ export default class HtsgetFile<
133
132
  baseUrl: string
134
133
  recordClass?: BamRecordClass<T>
135
134
  /**
136
- * fetch implementation used for every request, so an `Authorization: Bearer
137
- * <token>` header can be added for servers that require one. It is also
138
- * called with the data-block urls from the ticket, which may point at
139
- * third-party hosts, so only attach credentials to hosts you trust — the
140
- * spec has servers put whatever a data block needs in that url's own
141
- * `headers` field, which is applied either way.
135
+ * fetch implementation for the **ticket request**, so an `Authorization:
136
+ * Bearer <token>` header can be added for endpoints that require one.
137
+ *
138
+ * The data blocks a ticket names are NOT fetched with it — they can point
139
+ * at any host, and the spec forbids sending the API's token to them. A
140
+ * block needing authorization carries it in the ticket's own `headers`
141
+ * field for that url, which is applied regardless.
142
142
  */
143
143
  fetch?: Fetcher
144
144
  /**
@@ -179,12 +179,14 @@ export default class HtsgetFile<
179
179
  * concatenated, which per the spec is a complete BAM stream.
180
180
  */
181
181
  private async fetchTicket(query: string, opts?: BaseOpts) {
182
- const url = `${this.baseUrl}/${this.trackId}?${query}`
182
+ // Exactly one slash between the two. An id may contain "/" and the spec's
183
+ // own examples start with one ("/byStudy/PRJEB4019"), while an endpoint is
184
+ // as often written with a trailing slash as without; concatenating raw
185
+ // produced "//" for either.
186
+ const url = `${this.baseUrl.replace(/\/+$/, '')}/${this.trackId.replace(/^\/+/, '')}?${query}`
183
187
  const res = await fetchOk(this.fetchFn, url, { signal: opts?.signal })
184
188
  const ticket: HtsgetTicket = await res.json()
185
- return fetchAndConcat(this.fetchFn, ticket.htsget.urls, {
186
- signal: opts?.signal,
187
- })
189
+ return fetchAndConcat(ticket.htsget.urls, { signal: opts?.signal })
188
190
  }
189
191
 
190
192
  async getRecordsForRange(
@@ -199,7 +201,7 @@ export default class HtsgetFile<
199
201
  return []
200
202
  }
201
203
  const uncba = await this.fetchTicket(
202
- `referenceName=${chr}&start=${min}&end=${max}&format=BAM`,
204
+ `referenceName=${encodeURIComponent(chr)}&start=${min}&end=${max}&format=BAM`,
203
205
  opts,
204
206
  )
205
207
  const zero = new VirtualOffset(0, 0)
package/src/record.ts CHANGED
@@ -418,9 +418,14 @@ export default class BamRecord {
418
418
  return this._dataView.getInt32(this._start + 8, true)
419
419
  }
420
420
 
421
+ // The end htslib's bam_endpos() reports: a record consuming no reference —
422
+ // an unmapped mate placed at its mate's coordinate, or an empty CIGAR —
423
+ // still covers one base rather than none, so a consumer's interval search on
424
+ // the base it sits at can find it (endpos() in util.ts applies the same rule
425
+ // to this library's own range filter).
421
426
  get end() {
422
427
  if (this._cachedEnd === undefined) {
423
- this._cachedEnd = this.start + this.length_on_ref
428
+ this._cachedEnd = this.start + Math.max(this.length_on_ref, 1)
424
429
  }
425
430
  return this._cachedEnd
426
431
  }