@gmod/bam 7.8.2 → 7.9.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +2 -2
- package/dist/bai.js +42 -17
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +4 -1
- package/dist/bamFile.js +40 -15
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +20 -0
- package/dist/csi.js.map +1 -1
- package/dist/index.d.ts +3 -1
- package/dist/indexFile.js +5 -2
- package/dist/indexFile.js.map +1 -1
- package/dist/record.d.ts +16 -5
- package/dist/record.js +151 -13
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +10 -0
- package/dist/util.js +18 -13
- package/dist/util.js.map +1 -1
- package/esm/bai.js +42 -17
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +4 -1
- package/esm/bamFile.js +40 -15
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +20 -0
- package/esm/csi.js.map +1 -1
- package/esm/index.d.ts +3 -1
- package/esm/indexFile.js +5 -2
- package/esm/indexFile.js.map +1 -1
- package/esm/record.d.ts +16 -5
- package/esm/record.js +151 -13
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +10 -0
- package/esm/util.js +18 -13
- package/esm/util.js.map +1 -1
- package/package.json +4 -1
- package/src/bai.ts +43 -17
- package/src/bamFile.ts +47 -21
- package/src/csi.ts +20 -0
- package/src/index.ts +6 -1
- package/src/indexFile.ts +5 -2
- package/src/record.ts +152 -20
- package/src/util.ts +18 -13
package/README.md
CHANGED
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@@ -65,8 +65,8 @@ const bam = new HtsgetFile({
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Your `fetch` is called for the ticket request and for the data-block urls the
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ticket points at, so only attach credentials to hosts you trust — data blocks
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may live on a third-party host, and the spec has servers put whatever those
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-
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may live on a third-party host, and the spec has servers put whatever those need
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in each url's own `headers` field, which is applied either way.
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## Documentation
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package/dist/bai.js
CHANGED
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@@ -47,15 +47,36 @@ const BAI_MAGIC = 21578050; // BAI\1
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// https://github.com/samtools/hts-specs/blob/master/SAMv1.pdf
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const BAI_LINEAR_SHIFT = 14;
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const BAI_LINEAR_INTERVAL = 1 << BAI_LINEAR_SHIFT; // 16384
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const BAI_DEPTH = 5;
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// Highest coordinate the scheme addresses: the deepest level's bins are
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// BAI_LINEAR_INTERVAL wide and there are 8^BAI_DEPTH of them.
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const BAI_MAX_POS = 2 ** (BAI_LINEAR_SHIFT + BAI_DEPTH * 3); // 2^29
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function roundDown(n, multiple) {
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return n - (n % multiple);
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}
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// Note the `rem === 0` case: without it a coordinate already on a window
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// boundary rounds up a whole extra window, which is enough to push indexCov's
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// range past the end of the linear index.
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function roundUp(n, multiple) {
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-
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const rem = n % multiple;
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return rem === 0 ? n : n - rem + multiple;
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}
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// Compute bin ranges that overlap [beg, end). Each level's first-bin offset
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// is (8^L - 1) / 7. See SAMv1.pdf §5.1.1 for the binning derivation.
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function reg2bins(beg, end) {
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// Clamp to what the scheme can address, the way CSI's reg2bins clamps to
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// its own. The shifts below are the `>>` operator, so a coordinate past
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// 2^31 wraps to a negative bin number and every level yields an empty
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// range: `getRecordsForRange(chr, 0, 2**32)` — a caller asking for a whole
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// reference without knowing its length — came back with NO records at all
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// rather than all of them. Clamping is also what keeps a merely-large end
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// from walking ~130k absent bin numbers before finding the same chunks.
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if (beg > BAI_MAX_POS) {
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beg = BAI_MAX_POS;
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}
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if (end > BAI_MAX_POS) {
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end = BAI_MAX_POS;
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}
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end -= 1;
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return [
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[0, 0],
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@@ -75,8 +96,7 @@ class BAI extends indexFile_ts_1.default {
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throw new Error('Not a BAI file');
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}
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const refCount = dataView.getInt32(4, true);
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const
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const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7;
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const binLimit = ((1 << ((BAI_DEPTH + 1) * 3)) - 1) / 7;
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// read the indexes for each reference sequence
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let curr = 8;
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let firstDataLine;
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@@ -97,11 +117,9 @@ class BAI extends indexFile_ts_1.default {
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}
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else {
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const chunkCount = dataView.getInt32(curr, true);
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curr += 8;
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}
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// 16 bytes per chunk (two virtual offsets); the first pass only
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// needs to step over them. Same shape as csi.ts's first pass.
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curr += 4 + 16 * chunkCount;
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}
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}
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// walk the linear index to find the smallest virtual offset, which
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@@ -183,7 +201,6 @@ class BAI extends indexFile_ts_1.default {
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}
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async indexCov(seqId, start, end, opts) {
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const v = BAI_LINEAR_INTERVAL;
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const range = start !== undefined;
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const indexData = await this.parse(opts);
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const seqIdx = indexData.indices(seqId);
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if (!seqIdx) {
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@@ -194,15 +211,23 @@ class BAI extends indexFile_ts_1.default {
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if (nintv === 0) {
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return [];
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}
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// The linear index describes [0, indexEnd): each window's score is the gap
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// to the NEXT entry, so the final entry is a boundary rather than a window
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// of its own. Both ends are clamped to it instead of throwing, so a range
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// query returns the part of the reference the index covers — asking for the
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// whole reference by its length (`indexCov(ref, 0, ctgLength)`, the obvious
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// call, and one where end lands in the last window) used to throw "query
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// outside of range of linear index" while `indexCov(ref)` answered fine.
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const indexEnd = (nintv - 1) * v;
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const s = start === undefined
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? 0
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: Math.min(Math.max(roundDown(start, v), 0), indexEnd);
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const e = end === undefined ? indexEnd : Math.min(roundUp(end, v), indexEnd);
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if (e <= s) {
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return [];
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}
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const depths = new Array((e - s) / v);
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const totalSize = linearBlockPositions[nintv - 1];
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// Scale the block-delta into a read count as we go, rather than building the
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// entries and then rebuilding every one of them to apply the scale. Keep the
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// multiply-then-divide order: hoisting lineCount/totalSize into a factor
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package/dist/bai.js.map
CHANGED
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@@ -1 +1 @@
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1
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+
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|
package/dist/bamFile.d.ts
CHANGED
|
@@ -23,14 +23,17 @@ interface ChunkEntry<T> {
|
|
|
23
23
|
}
|
|
24
24
|
export declare const DEFAULT_MAX_CACHE_BYTES: number;
|
|
25
25
|
declare class ChunkFeatureCache<T> {
|
|
26
|
-
|
|
26
|
+
private _maxBytes;
|
|
27
27
|
private entries;
|
|
28
28
|
private bytes;
|
|
29
29
|
constructor(maxBytes: number);
|
|
30
|
+
get maxBytes(): number;
|
|
31
|
+
set maxBytes(maxBytes: number);
|
|
30
32
|
get size(): number;
|
|
31
33
|
get byteSize(): number;
|
|
32
34
|
get(key: string): ChunkEntry<T> | undefined;
|
|
33
35
|
set(key: string, entry: ChunkEntry<T>): void;
|
|
36
|
+
private evict;
|
|
34
37
|
delete(key: string): void;
|
|
35
38
|
clear(): void;
|
|
36
39
|
[Symbol.iterator](): MapIterator<[string, ChunkEntry<T>]>;
|
package/dist/bamFile.js
CHANGED
|
@@ -15,10 +15,13 @@ const sam_ts_1 = require("./sam.js");
|
|
|
15
15
|
const util_ts_1 = require("./util.js");
|
|
16
16
|
exports.BAM_MAGIC = 21840194;
|
|
17
17
|
const blockLen = 1 << 16;
|
|
18
|
-
// Ceiling on the header read. A million contigs is roughly 10MB of
|
|
19
|
-
// @SQ lines and ref-seq table, so
|
|
20
|
-
// claiming a huge n_ref rather than a real one, and
|
|
21
|
-
// just downloads the file.
|
|
18
|
+
// Ceiling on GROWING the header read. A million contigs is roughly 10MB of
|
|
19
|
+
// compressed @SQ lines and ref-seq table, so a read that has doubled past this
|
|
20
|
+
// is chasing a corrupt header claiming a huge n_ref rather than a real one, and
|
|
21
|
+
// growing further just downloads the file. It does not cap the FIRST read: that
|
|
22
|
+
// length comes from the index's firstDataLine, which is a real offset rather
|
|
23
|
+
// than a guess, so a header that genuinely runs past this still gets its one
|
|
24
|
+
// exact read. See getHeaderPre.
|
|
22
25
|
const maxHeaderReadLen = 32 * 1024 * 1024;
|
|
23
26
|
function resolveFilehandle(filehandle, path, url) {
|
|
24
27
|
return (filehandle ??
|
|
@@ -65,11 +68,21 @@ exports.DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
|
|
|
65
68
|
// nothing on the transport that matters and only widens peak memory.
|
|
66
69
|
const MAX_CONCURRENT_CHUNK_READS = 6;
|
|
67
70
|
class ChunkFeatureCache {
|
|
68
|
-
|
|
71
|
+
_maxBytes;
|
|
69
72
|
entries = new Map();
|
|
70
73
|
bytes = 0;
|
|
71
74
|
constructor(maxBytes) {
|
|
72
|
-
this.
|
|
75
|
+
this._maxBytes = maxBytes;
|
|
76
|
+
}
|
|
77
|
+
get maxBytes() {
|
|
78
|
+
return this._maxBytes;
|
|
79
|
+
}
|
|
80
|
+
// Accessor rather than a plain field so lowering the budget frees memory now.
|
|
81
|
+
// As a field, a caller trimming the cache under memory pressure got nothing
|
|
82
|
+
// back until the next chunk read happened to call set().
|
|
83
|
+
set maxBytes(maxBytes) {
|
|
84
|
+
this._maxBytes = maxBytes;
|
|
85
|
+
this.evict();
|
|
73
86
|
}
|
|
74
87
|
get size() {
|
|
75
88
|
return this.entries.size;
|
|
@@ -90,11 +103,14 @@ class ChunkFeatureCache {
|
|
|
90
103
|
this.delete(key);
|
|
91
104
|
this.entries.set(key, entry);
|
|
92
105
|
this.bytes += entry.bytes;
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
106
|
+
this.evict();
|
|
107
|
+
}
|
|
108
|
+
// Evict from the least-recently-used end. The size > 1 guard means a single
|
|
109
|
+
// chunk larger than the whole budget is still kept: the caller needs it for
|
|
110
|
+
// the query in flight, and dropping it would only force a re-decompress.
|
|
111
|
+
evict() {
|
|
96
112
|
const lru = this.entries.keys();
|
|
97
|
-
while (this.bytes > this.
|
|
113
|
+
while (this.bytes > this._maxBytes && this.entries.size > 1) {
|
|
98
114
|
this.delete(lru.next().value);
|
|
99
115
|
}
|
|
100
116
|
}
|
|
@@ -177,16 +193,21 @@ class BamFile {
|
|
|
177
193
|
let readLen = indexData.firstDataLine === undefined
|
|
178
194
|
? blockLen
|
|
179
195
|
: indexData.firstDataLine.blockPosition + blockLen;
|
|
196
|
+
// do/while, so the index-derived length is always read once and only the
|
|
197
|
+
// doubling is bounded. Testing readLen before the first read instead meant
|
|
198
|
+
// a BAM whose header genuinely exceeds maxHeaderReadLen — millions of
|
|
199
|
+
// contigs — was rejected without a single byte being fetched, and reported
|
|
200
|
+
// as 'Insufficient data for reference sequences' when the data was there.
|
|
180
201
|
let samHeader;
|
|
181
|
-
let atEof
|
|
182
|
-
|
|
202
|
+
let atEof;
|
|
203
|
+
do {
|
|
183
204
|
const buffer = await this.bam.read(readLen, 0, { signal: opts.signal });
|
|
184
205
|
// a short read means readLen ran past the end of the file, so there are
|
|
185
206
|
// no more bytes to grow into
|
|
186
207
|
atEof = buffer.length < readLen;
|
|
187
208
|
samHeader = this.applyHeader(await (0, bgzf_filehandle_1.unzip)(buffer));
|
|
188
209
|
readLen *= 2;
|
|
189
|
-
}
|
|
210
|
+
} while (samHeader === undefined && !atEof && readLen <= maxHeaderReadLen);
|
|
190
211
|
if (samHeader === undefined) {
|
|
191
212
|
throw new Error('Insufficient data for reference sequences');
|
|
192
213
|
}
|
|
@@ -453,8 +474,12 @@ class BamFile {
|
|
|
453
474
|
const mateRecs = [];
|
|
454
475
|
for (let i = 0, l = features.length; i < l; i++) {
|
|
455
476
|
const feature = features[i];
|
|
456
|
-
|
|
457
|
-
|
|
477
|
+
// fileOffset first: it is a number already on the record, where
|
|
478
|
+
// `name` decodes a string per record. A mate chunk usually overlaps
|
|
479
|
+
// the query region, so this skips the decode for every record the
|
|
480
|
+
// caller is already holding.
|
|
481
|
+
if (!readIds.has(feature.fileOffset) &&
|
|
482
|
+
readNameCounts.get(feature.name) === 1) {
|
|
458
483
|
mateRecs.push(feature);
|
|
459
484
|
}
|
|
460
485
|
}
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/csi.js
CHANGED
|
@@ -104,6 +104,20 @@ class CSI extends indexFile_ts_1.default {
|
|
|
104
104
|
this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
|
|
105
105
|
const maxBinNumber = this.maxBinNumber;
|
|
106
106
|
const auxLength = dataView.getInt32(12, true);
|
|
107
|
+
// A tabix-only branch, which is why parseAuxData and the parseNameBytes it
|
|
108
|
+
// calls show as uncovered. CSI is shared between `samtools index -c` and
|
|
109
|
+
// `tabix -C`, and the aux block is how a tabix index carries what a reader
|
|
110
|
+
// of bgzipped TEXT needs: which columns hold ref/start/end, the comment
|
|
111
|
+
// character, lines to skip, and the reference names — which a BAM takes
|
|
112
|
+
// from its own header instead. So a BAM .csi sets l_aux to 0 and never
|
|
113
|
+
// reaches here (checked: 0 of the 19 .csi fixtures carry one).
|
|
114
|
+
//
|
|
115
|
+
// Kept rather than deleted for two reasons. CSI is exported from
|
|
116
|
+
// index.ts, so pointing it at a tabix index is reachable (@gmod/tabix is
|
|
117
|
+
// the right tool, but this would half-work and then silently not).
|
|
118
|
+
// More importantly parseNameBytes is marked SYNC: with its tabix-js
|
|
119
|
+
// counterpart, and dropping one side of a deliberately-paired pair of
|
|
120
|
+
// implementations is exactly what that marker exists to prevent.
|
|
107
121
|
const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
|
|
108
122
|
const refCount = dataView.getInt32(16 + auxLength, true);
|
|
109
123
|
// SYNC: ~/src/gmod/tabix-js/src/csi.ts _parse — two-pass structure
|
|
@@ -204,6 +218,12 @@ class CSI extends indexFile_ts_1.default {
|
|
|
204
218
|
for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {
|
|
205
219
|
const b = t + rshift(beg, s);
|
|
206
220
|
const e = t + rshift(end, s);
|
|
221
|
+
// Unreachable as long as the clamp above stands, which is why it shows
|
|
222
|
+
// as uncovered: with end bounded to 2^(minShift + depth*3), level l
|
|
223
|
+
// spans at most 8^l - 1 bins, so the worst case is 8^depth - 1 + depth
|
|
224
|
+
// against a maxBinNumber of (8^(depth+1) - 1)/7, i.e. about 1.14 * 8^depth.
|
|
225
|
+
// Kept as a guard on the arithmetic rather than deleted — reg2bins is
|
|
226
|
+
// shared with tabix-js, whose callers reach it by other routes.
|
|
207
227
|
if (e - b + bins.length > this.maxBinNumber) {
|
|
208
228
|
throw new Error(`query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
|
|
209
229
|
}
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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AAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,IAAA,wBAAc,EAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,OAAO;gBACL,QAAQ;gBACR,KAAK,EAAE,cAAc;aACtB,CAAA;QACH,CAAC;QAED,OAAO;YACL,aAAa;YACb,OAAO,EAAE,IAAA,6BAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;YACR,GAAG,EAAE,IAAI;YACT,GAAG,GAAG;SACP,CAAA;IACH,CAAC;IAED,2EAA2E;IACjE,cAAc;QACtB,OAAO,WAAW,CAAA;IACpB,CAAC;IAED;;;;OAIG;IACH,gDAAgD;IACtC,QAAQ,CAAC,GAAW,EAAE,GAAW;QACzC,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,MAAM,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QACpD,IAAI,GAAG,GAAG,MAAM,EAAE,CAAC;YACjB,GAAG,GAAG,MAAM,CAAA;QACd,CAAC;QACD,GAAG,IAAI,CAAC,CAAA;QACR,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,OAAO,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,uEAAuE;YACvE,oEAAoE;YACpE,uEAAuE;YACvE,4EAA4E;YAC5E,sEAAsE;YACtE,gEAAgE;YAChE,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,IAAI,GAAG,mDAAmD,IAAI,CAAC,QAAQ,WAAW,IAAI,CAAC,KAAK,0DAA0D,CACnK,CAAA;YACH,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAU,CAAC,CAAA;QAC5B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF;AA7MD,sBA6MC"}
|
package/dist/index.d.ts
CHANGED
|
@@ -3,6 +3,8 @@ export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts';
|
|
|
3
3
|
export { default as CSI } from './csi.ts';
|
|
4
4
|
export { default as BamRecord } from './record.ts';
|
|
5
5
|
export { default as HtsgetFile } from './htsget.ts';
|
|
6
|
-
export type {
|
|
6
|
+
export type { NumericCigar } from './record.ts';
|
|
7
7
|
export type { BamRecordClass, BamRecordLike } from './bamFile.ts';
|
|
8
|
+
export type { BamOpts, BaseOpts } from './util.ts';
|
|
9
|
+
export type { IndexCovEntry } from './bai.ts';
|
|
8
10
|
export type { Fetcher } from 'generic-filehandle2';
|
package/dist/indexFile.js
CHANGED
|
@@ -12,8 +12,11 @@ const util_ts_1 = require("./util.js");
|
|
|
12
12
|
function memoizeByRefId(getIndices, maxSize = 5) {
|
|
13
13
|
const cache = new quick_lru_1.default({ maxSize });
|
|
14
14
|
return (refId) => {
|
|
15
|
-
|
|
16
|
-
|
|
15
|
+
// one lookup, not has()+get(): only truthy results are ever cached, so a
|
|
16
|
+
// miss and a cached value are already distinguishable
|
|
17
|
+
const cached = cache.get(refId);
|
|
18
|
+
if (cached !== undefined) {
|
|
19
|
+
return cached;
|
|
17
20
|
}
|
|
18
21
|
const result = getIndices(refId);
|
|
19
22
|
if (result) {
|
package/dist/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;AA6BA,
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;AA6BA,wCAkBC;AA/CD,mEAAyC;AAEzC,uCAA0C;AAwB1C,uDAAuD;AACvD,6EAA6E;AAC7E,2CAA2C;AAC3C,SAAgB,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,KAAK,GAAG,IAAI,mBAAQ,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAClD,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,yEAAyE;QACzE,sDAAsD;QACtD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC/B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,EAAE,CAAC;YACX,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1B,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC;AAED,MAA8B,SAAS;IAG9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAElC,MAAM,CAAmB;IAEjC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAwBD,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAY,EAAE,CAAA;QAC1B,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAC/B,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;wBACjD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,IAAI,CAAC,cAAc,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,CAAA;IAC7D,CAAC;IAED,KAAK,CAAC,OAAiB,EAAE;QACvB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IACnC,CAAC;IAED,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,IAAA,wBAAc,EAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AA5GD,4BA4GC"}
|
package/dist/record.d.ts
CHANGED
|
@@ -1,9 +1,4 @@
|
|
|
1
1
|
export type NumericCigar = Uint32Array | Int32Array | number[];
|
|
2
|
-
export interface Bytes {
|
|
3
|
-
start: number;
|
|
4
|
-
end: number;
|
|
5
|
-
byteArray: Uint8Array;
|
|
6
|
-
}
|
|
7
2
|
export default class BamRecord {
|
|
8
3
|
fileOffset: number;
|
|
9
4
|
private _byteArray;
|
|
@@ -34,6 +29,22 @@ export default class BamRecord {
|
|
|
34
29
|
get tags(): Record<string, unknown>;
|
|
35
30
|
getTag(tagName: string): unknown;
|
|
36
31
|
getTagRaw(tagName: string): unknown;
|
|
32
|
+
/**
|
|
33
|
+
* The value of `tagName`, or of `altName` if the record carries no `tagName` —
|
|
34
|
+
* resolved in ONE pass over the tag block instead of two.
|
|
35
|
+
*
|
|
36
|
+
* For the MM/Mm and ML/Ml alias pairs that modified-base callers emit, where
|
|
37
|
+
* `getTag(a) ?? getTag(b)` walks every tag on the record TWICE whenever
|
|
38
|
+
* neither is present, which is every read in a file without base
|
|
39
|
+
* modifications. jbrowse-components issues exactly that lookup per record on
|
|
40
|
+
* every render (extractModifications runs unconditionally), and on
|
|
41
|
+
* jb2bench's 1000x.shortread it was 12.9% of the whole query — more than the
|
|
42
|
+
* CIGAR, SEQ and MD reads the pileup actually uses, spent proving absence.
|
|
43
|
+
*
|
|
44
|
+
* `tagName` wins wherever it appears, so the result matches the two-lookup
|
|
45
|
+
* form even for a (malformed) record carrying both.
|
|
46
|
+
*/
|
|
47
|
+
getTagAlt(tagName: string, altName: string): unknown;
|
|
37
48
|
private _findTag;
|
|
38
49
|
private _computeTags;
|
|
39
50
|
isPaired(): boolean;
|