From 4576be0bbcfbbc3c57dff0e529d5aea7ceb4a7c3 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 6 Nov 2024 20:05:38 -0500 Subject: [PATCH] Refactor bam features --- CHANGELOG.md | 11 +- README.md | 2 +- package.json | 3 +- src/bamFile.ts | 20 +- src/record.ts | 384 ++++------ test/__snapshots__/bai.test.ts.snap | 405 ++--------- test/bai.test.ts | 109 ++- test/csi.test.ts | 4 +- test/fakerecord.ts | 15 +- test/vanilla-node.test.ts | 14 +- yarn.lock | 1043 +++++++++++++-------------- 11 files changed, 807 insertions(+), 1203 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3b36709..c8ac387 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,16 +1,13 @@ ## [2.0.4](https://github.com/GMOD/bam-js/compare/v2.0.3...v2.0.4) (2024-08-09) - - ## [2.0.3](https://github.com/GMOD/bam-js/compare/v2.0.2...v2.0.3) (2024-07-23) - ### Reverts -* Revert "Migrate to eslint9" ([65adcbb](https://github.com/GMOD/bam-js/commit/65adcbb2793243659682d30694f8604d241a5337)) -* Revert "Run format" ([2a02535](https://github.com/GMOD/bam-js/commit/2a02535db4df80f245232522cdba771cbf5ea214)) - - +- Revert "Migrate to eslint9" + ([65adcbb](https://github.com/GMOD/bam-js/commit/65adcbb2793243659682d30694f8604d241a5337)) +- Revert "Run format" + ([2a02535](https://github.com/GMOD/bam-js/commit/2a02535db4df80f245232522cdba771cbf5ea214)) ## [2.0.2](https://github.com/GMOD/bam-js/compare/v2.0.1...v2.0.2) (2024-02-21) diff --git a/README.md b/README.md index 96544ca..f8db6c6 100644 --- a/README.md +++ b/README.md @@ -161,7 +161,7 @@ feature.get('end') // 0-based half open end coordinate feature.get('name') // QNAME feature.get('seq') // feature sequence feature.get('qual') // qualities -feature.get('cigar') // cigar string +feature.get('CIGAR') // CIGAR string feature.get('MD') // MD string feature.get('SA') // supplementary alignments feature.get('template_length') // TLEN diff --git a/package.json b/package.json index ce28a49..35bbc8b 100644 --- a/package.json +++ b/package.json @@ -40,6 +40,7 @@ "dependencies": { "@gmod/abortable-promise-cache": "^2.0.0", "@gmod/bgzf-filehandle": "^1.4.4", + "buffer": "^6.0.3", "crc": "^4.3.2", "generic-filehandle": "^3.0.0", "quick-lru": "^4.0.0" @@ -53,7 +54,7 @@ "eslint": "^9.9.0", "eslint-config-prettier": "^9.1.0", "eslint-plugin-prettier": "^5.1.3", - "eslint-plugin-unicorn": "^55.0.0", + "eslint-plugin-unicorn": "^56.0.0", "prettier": "^3.2.5", "rimraf": "^6.0.1", "standard-changelog": "^6.0.0", diff --git a/src/bamFile.ts b/src/bamFile.ts index 0c61ba0..c157270 100644 --- a/src/bamFile.ts +++ b/src/bamFile.ts @@ -288,12 +288,12 @@ export default class BamFile { const recs = [] as BAMFeature[] for (const feature of records) { - if (feature.seq_id() === chrId) { - if (feature.get('start') >= max) { + if (feature.ref_id === chrId) { + if (feature.start >= max) { // past end of range, can stop iterating done = true break - } else if (feature.get('end') >= min) { + } else if (feature.end >= min) { // must be in range recs.push(feature) } @@ -319,8 +319,8 @@ export default class BamFile { feats.map(ret => { const readNames: Record = {} for (const element of ret) { - const name = element.name() - const id = element.id() + const name = element.name + const id = element.id if (!readNames[name]) { readNames[name] = 0 } @@ -337,10 +337,10 @@ export default class BamFile { const matePromises: Promise[] = [] feats.map(ret => { for (const f of ret) { - const name = f.name() - const start = f.get('start') - const pnext = f._next_pos() - const rnext = f._next_refid() + const name = f.name + const start = f.start + const pnext = f.next_pos + const rnext = f.next_refid if ( this.index && unmatedPairs[name] && @@ -377,7 +377,7 @@ export default class BamFile { dpositions, chunk, )) { - if (unmatedPairs[feature.get('name')] && !readIds[feature.id()]) { + if (unmatedPairs[feature.name] && !readIds[feature.id]) { mateRecs.push(feature) } } diff --git a/src/record.ts b/src/record.ts index 4ca8cd9..63fb910 100644 --- a/src/record.ts +++ b/src/record.ts @@ -1,202 +1,110 @@ import Constants from './constants' +import type { Buffer } from 'buffer' const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('') const CIGAR_DECODER = 'MIDNSHP=X???????'.split('') -/** - * Class of each BAM record returned by this API. - */ +interface Bytes { + start: number + end: number + byteArray: Buffer +} export default class BamRecord { - private data = {} as Record - private bytes: { start: number; end: number; byteArray: Buffer } - private _id: number - private _tagOffset: number | undefined - private _tagList: string[] = [] - private _allTagsParsed = false - - public flags: any - public _refID: number - constructor(args: any) { - const { bytes, fileOffset } = args - const { byteArray, start } = bytes - this.data = { start: byteArray.readInt32LE(start + 8) } - this.bytes = bytes - this._id = fileOffset - this._refID = byteArray.readInt32LE(start + 4) - this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16 - } - - get(field: string) { - //@ts-ignore - if (this[field]) { - //@ts-ignore - if (this.data[field]) { - return this.data[field] - } - //@ts-ignore - this.data[field] = this[field]() - return this.data[field] - } - return this._get(field.toLowerCase()) - } + public fileOffset: number + private bytes: Bytes - end() { - return this.get('start') + this.get('length_on_ref') + constructor(args: { bytes: Bytes; fileOffset: number }) { + this.bytes = args.bytes + this.fileOffset = args.fileOffset } - seq_id() { - return this._refID + get byteArray() { + return this.bytes.byteArray } - // same as get(), except requires lower-case arguments. used - // internally to save lots of calls to field.toLowerCase() - _get(field: string) { - if (field in this.data) { - return this.data[field] - } - this.data[field] = this._parseTag(field) - return this.data[field] - } - - _tags() { - this._parseAllTags() - - let tags = ['seq'] - - if (!this.isSegmentUnmapped()) { - tags.push( - 'start', - 'end', - 'strand', - 'score', - 'qual', - 'MQ', - 'CIGAR', - 'length_on_ref', - 'template_length', - ) - } - if (this.isPaired()) { - tags.push('next_segment_position', 'pair_orientation') - } - tags = tags.concat(this._tagList) - - for (const k of Object.keys(this.data)) { - if (!k.startsWith('_') && k !== 'next_seq_id') { - tags.push(k) - } - } - - const seen: Record = {} - return tags.filter(t => { - if ( - (t in this.data && this.data[t] === undefined) || - t === 'CG' || - t === 'cg' - ) { - return false - } - - const lt = t.toLowerCase() - const s = seen[lt] - seen[lt] = true - return !s - }) + get flags() { + return ( + (this.byteArray.readInt32LE(this.bytes.start + 16) & 0xffff0000) >> 16 + ) + } + get ref_id() { + return this.byteArray.readInt32LE(this.bytes.start + 4) } - parent() { - return + get start() { + return this.byteArray.readInt32LE(this.bytes.start + 8) } - children() { - return this.get('subfeatures') + get end() { + return this.start + this.length_on_ref } - id() { - return this._id + get id() { + return this.fileOffset } - // special parsers - /** - * Mapping quality score. - */ - mq() { - const mq = (this.get('_bin_mq_nl') & 0xff00) >> 8 + get mq() { + const mq = (this.bin_mq_nl & 0xff00) >> 8 return mq === 255 ? undefined : mq } - score() { - return this.get('mq') + get score() { + return this.mq } - qual() { - return this.qualRaw()?.join(' ') + get qual() { + return this.qualRaw?.join(' ') } - qualRaw() { + get qualRaw() { if (this.isSegmentUnmapped()) { return } - const { start, byteArray } = this.bytes const p = - start + - 36 + - this.get('_l_read_name') + - this.get('_n_cigar_op') * 4 + - this.get('_seq_bytes') - const lseq = this.get('seq_length') - return byteArray.subarray(p, p + lseq) + this.b0 + + this.read_name_length + + this.num_CIGAR_ops * 4 + + this.num_seq_bytes + return this.byteArray.subarray(p, p + this.seq_length) } - strand() { + get strand() { return this.isReverseComplemented() ? -1 : 1 } - multi_segment_next_segment_strand() { - if (this.isMateUnmapped()) { - return - } - return this.isMateReverseComplemented() ? -1 : 1 + get multi_segment_next_segment_strand() { + return this.isMateUnmapped() + ? undefined + : this.isMateReverseComplemented() + ? -1 + : 1 } - name() { - return this.get('_read_name') + get b0() { + return this.bytes.start + 36 } - - _read_name() { - const nl = this.get('_l_read_name') - const { byteArray, start } = this.bytes - return byteArray.toString('ascii', start + 36, start + 36 + nl - 1) + get name() { + return this.byteArray.toString( + 'ascii', + this.b0, + this.b0 + this.read_name_length - 1, + ) } - /** - * Get the value of a tag, parsing the tags as far as necessary. - * Only called if we have not already parsed that field. - */ - _parseTag(tagName?: string) { - // if all of the tags have been parsed and we're still being - // called, we already know that we have no such tag, because - // it would already have been cached. - if (this._allTagsParsed) { - return - } - - const { byteArray, start } = this.bytes + get tags() { + const { byteArray } = this.bytes let p = - this._tagOffset || - start + - 36 + - this.get('_l_read_name') + - this.get('_n_cigar_op') * 4 + - this.get('_seq_bytes') + - this.get('seq_length') + this.b0 + + this.read_name_length + + this.num_CIGAR_ops * 4 + + this.num_seq_bytes + + this.seq_length const blockEnd = this.bytes.end - let lcTag - while (p < blockEnd && lcTag !== tagName) { + const tags = {} as Record + while (p < blockEnd) { const tag = String.fromCharCode(byteArray[p], byteArray[p + 1]) - lcTag = tag.toLowerCase() const type = String.fromCharCode(byteArray[p + 2]) p += 3 @@ -353,31 +261,9 @@ export default class BamRecord { } // stop parsing tags } - this._tagOffset = p - - this._tagList.push(tag) - if (lcTag === tagName) { - return value - } - - this.data[lcTag] = value + tags[tag] = value } - this._allTagsParsed = true - return - } - - _parseAllTags() { - this._parseTag('') - } - - _parseCigar(cigar: string) { - return ( - //@ts-ignore - cigar - .match(/\d+\D/g) - //@ts-ignore - .map(op => [/\D/.exec(op)[0].toUpperCase(), Number.parseInt(op, 10)]) - ) + return tags } /** @@ -443,26 +329,64 @@ export default class BamRecord { return !!(this.flags & Constants.BAM_FSUPPLEMENTARY) } - cigar() { + get CIGAR() { if (this.isSegmentUnmapped()) { - return + return '' } - const { byteArray, start } = this.bytes - const numCigarOps = this.get('_n_cigar_op') - let p = start + 36 + this.get('_l_read_name') - const seqLen = this.get('seq_length') - let cigar = '' + const { byteArray } = this.bytes + const numCigarOps = this.num_CIGAR_ops + let p = this.b0 + this.read_name_length + let CIGAR = '' + + // check for CG tag by inspecting whether the CIGAR field contains a clip + // that consumes entire seqLen + let cigop = byteArray.readInt32LE(p) + let lop = cigop >> 4 + let op = CIGAR_DECODER[cigop & 0xf] + if (op === 'S' && lop === this.seq_length) { + // if there is a CG the second CIGAR field will be a N tag the represents + // the length on ref + p += 4 + cigop = byteArray.readInt32LE(p) + lop = cigop >> 4 + op = CIGAR_DECODER[cigop & 0xf] + if (op !== 'N') { + console.warn('CG tag with no N tag') + } + return this.tags.CG as string + } else { + for (let c = 0; c < numCigarOps; ++c) { + cigop = byteArray.readInt32LE(p) + lop = cigop >> 4 + op = CIGAR_DECODER[cigop & 0xf] + CIGAR += lop + op + + p += 4 + } + + return CIGAR + } + } + + get length_on_ref() { + if (this.isSegmentUnmapped()) { + return 0 + } + + const { byteArray } = this.bytes + const numCigarOps = this.num_CIGAR_ops + let p = this.b0 + this.read_name_length let lref = 0 - // check for CG tag by inspecting whether the CIGAR field - // contains a clip that consumes entire seqLen + // check for CG tag by inspecting whether the CIGAR field contains a clip + // that consumes entire seqLen let cigop = byteArray.readInt32LE(p) let lop = cigop >> 4 let op = CIGAR_DECODER[cigop & 0xf] - if (op === 'S' && lop === seqLen) { - // if there is a CG the second CIGAR field will - // be a N tag the represents the length on ref + if (op === 'S' && lop === this.seq_length) { + // if there is a CG the second CIGAR field will be a N tag the represents + // the length on ref p += 4 cigop = byteArray.readInt32LE(p) lop = cigop >> 4 @@ -470,17 +394,15 @@ export default class BamRecord { if (op !== 'N') { console.warn('CG tag with no N tag') } - this.data.length_on_ref = lop - return this.get('CG') + return lop } else { for (let c = 0; c < numCigarOps; ++c) { cigop = byteArray.readInt32LE(p) lop = cigop >> 4 op = CIGAR_DECODER[cigop & 0xf] - cigar += lop + op - // soft clip, hard clip, and insertion don't count toward - // the length on the reference + // soft clip, hard clip, and insertion don't count toward the length on + // the reference if (op !== 'H' && op !== 'S' && op !== 'I') { lref += lop } @@ -488,45 +410,27 @@ export default class BamRecord { p += 4 } - this.data.length_on_ref = lref - return cigar + return lref } } - length_on_ref() { - if (this.data.length_on_ref) { - return this.data.length_on_ref - } else { - this.get('cigar') // the length_on_ref is set as a side effect - return this.data.length_on_ref - } + get num_CIGAR_ops() { + return this.flag_nc & 0xffff } - _n_cigar_op() { - return this.get('_flag_nc') & 0xffff + get read_name_length() { + return this.bin_mq_nl & 0xff } - _l_read_name() { - return this.get('_bin_mq_nl') & 0xff + get num_seq_bytes() { + return (this.seq_length + 1) >> 1 } - /** - * number of bytes in the sequence field - */ - _seq_bytes() { - return (this.get('seq_length') + 1) >> 1 - } - - getReadBases() { - return this.seq() - } - - seq() { - const { byteArray, start } = this.bytes - const p = - start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4 - const seqBytes = this.get('_seq_bytes') - const len = this.get('seq_length') + get seq() { + const { byteArray } = this.bytes + const p = this.b0 + this.read_name_length + this.num_CIGAR_ops * 4 + const seqBytes = this.num_seq_bytes + const len = this.seq_length let buf = '' let i = 0 for (let j = 0; j < seqBytes; ++j) { @@ -542,11 +446,11 @@ export default class BamRecord { } // adapted from igv.js - getPairOrientation() { + get pair_orientation() { if ( !this.isSegmentUnmapped() && !this.isMateUnmapped() && - this._refID === this._next_refid() + this.ref_id === this.next_refid ) { const s1 = this.isReverseComplemented() ? 'R' : 'F' const s2 = this.isMateReverseComplemented() ? 'R' : 'F' @@ -561,7 +465,7 @@ export default class BamRecord { } const tmp = [] - const isize = this.template_length() + const isize = this.template_length if (isize > 0) { tmp[0] = s1 tmp[1] = o1 @@ -578,28 +482,28 @@ export default class BamRecord { return '' } - _bin_mq_nl() { - return this.bytes.byteArray.readInt32LE(this.bytes.start + 12) + get bin_mq_nl() { + return this.byteArray.readInt32LE(this.bytes.start + 12) } - _flag_nc() { - return this.bytes.byteArray.readInt32LE(this.bytes.start + 16) + get flag_nc() { + return this.byteArray.readInt32LE(this.bytes.start + 16) } - seq_length() { - return this.bytes.byteArray.readInt32LE(this.bytes.start + 20) + get seq_length() { + return this.byteArray.readInt32LE(this.bytes.start + 20) } - _next_refid() { - return this.bytes.byteArray.readInt32LE(this.bytes.start + 24) + get next_refid() { + return this.byteArray.readInt32LE(this.bytes.start + 24) } - _next_pos() { - return this.bytes.byteArray.readInt32LE(this.bytes.start + 28) + get next_pos() { + return this.byteArray.readInt32LE(this.bytes.start + 28) } - template_length() { - return this.bytes.byteArray.readInt32LE(this.bytes.start + 32) + get template_length() { + return this.byteArray.readInt32LE(this.bytes.start + 32) } toJSON() { diff --git a/test/__snapshots__/bai.test.ts.snap b/test/__snapshots__/bai.test.ts.snap index d8e4c78..953c9e1 100644 --- a/test/__snapshots__/bai.test.ts.snap +++ b/test/__snapshots__/bai.test.ts.snap @@ -85,270 +85,61 @@ exports[`check ecoli header and records 1`] = ` exports[`check ecoli header and records 2`] = ` [ { - "data": { - "_bin_mq_nl": 306839109, - "_flag_nc": 113, - "_l_read_name": 69, - "_n_cigar_op": 113, - "cigar": "21M1I6M1I3M1I4M1I10M1I33M1I19M1I8M1I5M1D1M1D8M1D12M1D15M1I12M1I3M2D12M1I6M1D1M1D18M1D3M1D1M1D7M1I3M1I9M1I15M1I1M1I1M1I6M1I3M2I3M1D2M1D9M1D10M1I12M1I31M1I29M1I9M1I11M1I7M1D9M1I1M1I7M1I3M1I20M1I2M1D10M1I6M1D2M1I7M1D7M1I5M1D7M1D7M1I3M1I4M1I7M2I37M", - "end": 533, - "length_on_ref": 533, - "seq_length": 552, - "start": 0, - }, - "flags": 0, - }, - { - "data": { - "_bin_mq_nl": 306839109, - "_flag_nc": 149, - "_l_read_name": 69, - "_n_cigar_op": 149, - "cigar": "22M1I10M1I1M1I22M1D1M1D1M1I3M1I6M1D1M1D8M1D25M2D10M1I5M1I3M1D11M1I7M1I31M1I31M1I2M1I8M1D11M1D13M1I36M1I1M2I1M2I3M1D1M3I13M1I20M1D20M2I2M1I4M1D1M1D3M1D2M1D16M1I7M1D30M1I4M1I7M1I1M1D2M1D28M1I6M1I6M1I26M1I5M1D17M1I15M1D33M1D11M1D9M1I2M2I3M1D5M1D4M1I13M1I10M1I3M1I4M1I16M1D3M1I10M1D18M1D12M1I11M1I17M1I6M1I17M1D15M1I1M1D3M2I4M1D14M1D14M", - "end": 799, - "length_on_ref": 799, - "seq_length": 817, - "start": 0, - }, - "flags": 0, - }, - { - "data": { - "_bin_mq_nl": 306839109, - "_flag_nc": 145, - "_l_read_name": 69, - "_n_cigar_op": 145, - "cigar": 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6666142, + }, + { + "fileOffset": 6673752, + }, + { + "fileOffset": 6682819, + }, + { + "fileOffset": 6691689, + }, + { + "fileOffset": 13886185, + }, + { + "fileOffset": 13898957, + }, + { + "fileOffset": 13899467, + }, + { + "fileOffset": 13906392, + }, + { + "fileOffset": 13913893, + }, + { + "fileOffset": 13917686, + }, + { + "fileOffset": 13922994, + }, + { + "fileOffset": 13926392, + }, + { + "fileOffset": 13934351, }, ] `; @@ -356,18 +147,7 @@ exports[`check ecoli header and records 2`] = ` exports[`deep check 1000 genomes bai 1`] = ` [ { - "data": { - "_bin_mq_nl": 306774051, - "_flag_nc": 9502722, - "_l_read_name": 35, - "_n_cigar_op": 2, - "cigar": "183S67M", - "end": 10066, - "length_on_ref": 67, - "seq_length": 250, - "start": 9999, - }, - "flags": 145, + "fileOffset": 636682, }, ] `; @@ -375,32 +155,10 @@ exports[`deep check 1000 genomes bai 1`] = ` exports[`deep check volvox-sorted.bam 1`] = ` [ { - "data": { - "_bin_mq_nl": 306783516, - "_flag_nc": 1, - "_l_read_name": 28, - "_n_cigar_op": 1, - "cigar": "100M", - "end": 102, - "length_on_ref": 100, - "seq_length": 100, - "start": 2, - }, - "flags": 0, - }, - { - "data": { - "_bin_mq_nl": 306783516, - "_flag_nc": 1, - "_l_read_name": 28, - "_n_cigar_op": 1, - "cigar": "100M", - "end": 107, - "length_on_ref": 100, - "seq_length": 100, - "start": 7, - }, - "flags": 0, + "fileOffset": 2501248, + }, + { + "fileOffset": 2501501, }, ] `; @@ -741,31 +499,20 @@ exports[`loads volvox-sorted.bam 1`] = ` `; exports[`long tag list 1`] = ` -[ - "seq", - "start", - "end", - "strand", - "score", - "qual", - "MQ", - "CIGAR", - "length_on_ref", - "template_length", - "AS", - "NM", - "XI", - "XS", - "XE", - "XR", - "MD", - "SV", - "QS", - "QE", - "CV", - "ID", - "KB", - "SB", - "seq_length", -] +{ + "AS": 1794, + "CV": 99.56829833984375, + "ID": 78190, + "KB": 96.84300231933594, + "MD": "37^G130^T6^T1^T17^T44T13^C118^G24^A2C24^G14G12^G70^A8^G25^T5^G10^G79^G6^T28^G22C15^C2^G22^A1^G56C15T28^G16^C18^G12^G18A58G2^C21^G15^C24^C49^G17^C9C1^A7G23^A106C8^G16C20^C17^G6C81^CC14^C12^C30^T3^C11C6^CC20^C17T19^T16^C81", + "NM": 286, + "QE": 1853, + "QS": 8, + "SB": 96.84300231933594, + "SV": 2, + "XE": 1794, + "XI": 0.8489000201225281, + "XR": 1845, + "XS": 0, +} `; diff --git a/test/bai.test.ts b/test/bai.test.ts index 3f8d9c9..288ee9c 100644 --- a/test/bai.test.ts +++ b/test/bai.test.ts @@ -42,18 +42,18 @@ test('gets features from volvox-sorted.bam', async () => { await ti.getHeader() const records = await ti.getRecordsForRange('ctgA', 0, 1000) expect(records.length).toEqual(131) - expect(records[0].get('start')).toEqual(2) - expect(records[0].get('end')).toEqual(102) - expect(records[0].get('cigar')).toEqual('100M') - expect(records[0].get('name')).toEqual('ctgA_3_555_0:0:0_2:0:0_102d') - expect(records[0].get('qual')).toEqual( + expect(records[0].start).toEqual(2) + expect(records[0].end).toEqual(102) + expect(records[0].CIGAR).toEqual('100M') + expect(records[0].name).toEqual('ctgA_3_555_0:0:0_2:0:0_102d') + expect(records[0].qual).toEqual( '17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17', ) - expect(records[0].get('md')).toEqual('100') - expect(records[0].getReadBases()).toEqual( + expect(records[0].tags.MD).toEqual('100') + expect(records[0].seq).toEqual( 'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG', ) - expect(records[0].get('seq')).toEqual( + expect(records[0].seq).toEqual( 'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG', ) }) @@ -125,9 +125,7 @@ test('BamFile with test_deletion_2_0.snps.bwa_align.sorted.grouped.bam', async ( const features = await b.getRecordsForRange('Chromosome', 17000, 18000) expect(features.length).toEqual(124) expect( - features.every( - feature => feature.get('seq_length') === feature.getReadBases().length, - ), + features.every(feature => feature.seq_length === feature.seq.length), ).toBeTruthy() }) @@ -158,10 +156,10 @@ test('BamFile with B tags', async () => { const features = await b.getRecordsForRange('chr1', 980654, 981663) // ZC:B:i,364,359,1,0 ZD:B:f,0.01,0.02,0.03 ZE:B:c,0,1,2,3 ZK:B:s,45,46,47 - const ret = features[1].get('ZD').split(',') - expect(features[1].get('ZC')).toEqual('364,359,1,0') - expect(features[1].get('ZE')).toEqual('0,1,2,3') - expect(features[1].get('ZK')).toEqual('45,46,47') + const ret = (features[1].tags.ZD as string).split(',') + expect(features[1].tags.ZC).toEqual('364,359,1,0') + expect(features[1].tags.ZE).toEqual('0,1,2,3') + expect(features[1].tags.ZK).toEqual('45,46,47') expect(+ret[0]).toBeCloseTo(0.01) expect(+ret[1]).toBeCloseTo(0.02) expect(+ret[2]).toBeCloseTo(0.03) @@ -174,8 +172,8 @@ test('paired ends', async () => { const features = await b.getRecordsForRange('20', 62500, 64500) const f = features[0] - expect(f._next_refid()).toEqual(19) - expect(f._next_pos()).toEqual(62352) + expect(f.next_refid).toEqual(19) + expect(f.next_pos).toEqual(62352) }) test('read as pairs', async () => { const b = new BamFile({ bamPath: 'test/data/paired.bam' }) @@ -188,12 +186,12 @@ test('read as pairs', async () => { viewAsPairs: true, }) const features2 = await p.getRecordsForRange('20', 0, 70000) - expect(features.map(f => f.get('name')).sort()).toEqual( - features2.map(f => f.get('name')).sort(), + expect(features.map(f => f.name).sort()).toEqual( + features2.map(f => f.name).sort(), ) const f = features[features.length - 1] const f2 = features2[features2.length - 1] - expect(f.get('start')).toEqual(f2.get('start')) + expect(f.start).toEqual(f2.start) }) test('test pair orientations', async () => { @@ -209,18 +207,18 @@ test('test pair orientations', async () => { const b10 = new FakeRecord(false, 'F', 'R', -100) const b11 = new FakeRecord(false, 'R', 'R', -100) const b12 = new FakeRecord(false, 'R', 'F', -100) - expect(b1.getPairOrientation()).toEqual('F1F2') - expect(b2.getPairOrientation()).toEqual('F1R2') - expect(b3.getPairOrientation()).toEqual('R1R2') - expect(b4.getPairOrientation()).toEqual('R1F2') - expect(b5.getPairOrientation()).toEqual('F2F1') - expect(b6.getPairOrientation()).toEqual('F2R1') - expect(b7.getPairOrientation()).toEqual('R2R1') - expect(b8.getPairOrientation()).toEqual('R2F1') - expect(b9.getPairOrientation()).toEqual('F1F2') - expect(b10.getPairOrientation()).toEqual('R1F2') - expect(b11.getPairOrientation()).toEqual('R1R2') - expect(b12.getPairOrientation()).toEqual('F1R2') + expect(b1.pair_orientation).toEqual('F1F2') + expect(b2.pair_orientation).toEqual('F1R2') + expect(b3.pair_orientation).toEqual('R1R2') + expect(b4.pair_orientation).toEqual('R1F2') + expect(b5.pair_orientation).toEqual('F2F1') + expect(b6.pair_orientation).toEqual('F2R1') + expect(b7.pair_orientation).toEqual('R2R1') + expect(b8.pair_orientation).toEqual('R2F1') + expect(b9.pair_orientation).toEqual('F1F2') + expect(b10.pair_orientation).toEqual('R1F2') + expect(b11.pair_orientation).toEqual('R1R2') + expect(b12.pair_orientation).toEqual('F1R2') }) test('SAM spec pdf', async () => { @@ -229,8 +227,8 @@ test('SAM spec pdf', async () => { const features = await b.getRecordsForRange('ref', 1, 100) expect(features.length).toEqual(6) - expect(features[2].get('sa')).toEqual('ref,29,-,6H5M,17,0;') - expect(features[4].get('sa')).toEqual('ref,9,+,5S6M,30,1;') + expect(features[2].tags.SA).toEqual('ref,29,-,6H5M,17,0;') + expect(features[4].tags.SA).toEqual('ref,9,+,5S6M,30,1;') }) test('trigger range out of bounds file', async () => { const b = new BamFile({ bamPath: 'test/data/cho.bam' }) @@ -257,7 +255,7 @@ test('unique id for duplicate features', async () => { const ti = new BamFile({ bamPath: 'test/data/exact_duplicate.bam' }) await ti.getHeader() const ret = await ti.getRecordsForRange('ctgA', 0, 1000) - expect(ret[0].id() !== ret[1].id()).toBeTruthy() + expect(ret[0].id !== ret[1].id).toBeTruthy() }) test('usage of the chr22 ultralong nanopore', async () => { @@ -266,17 +264,17 @@ test('usage of the chr22 ultralong nanopore', async () => { const ret1 = await ti.getRecordsForRange('22', 16559999, 16564499) const ret2 = await ti.getRecordsForRange('22', 16564499, 16564999) const [r1, r2] = [ret1, ret2].map(x => - x.find(k => k.get('name') === '3d509937-5c54-46d7-8dec-c49c7165d2d5'), + x.find(k => k.name === '3d509937-5c54-46d7-8dec-c49c7165d2d5'), ) - expect(r1?.getReadBases()).toEqual(r2?.getReadBases()) - expect(r1?.getReadBases()).toBe( + expect(r1?.seq).toEqual(r2?.seq) + expect(r1?.seq).toBe( 'TCTTCAGACCCTCGAAACAGTGTTCTGAAATCCTATGGCAGGGAACAACAGAACCCAGCCACTGTGTGCTGGAATCCTGTCTGAGGACAAACATTCAAACACTCATGAAAGTGTTCTGGAATCTTATGTGAGTGATAAGCAATCAGAAACCAGCAGCGGTGCTCTGTAATCCTTTGTGAGGACAAACAGTACACAGAGCAAGTTCTGGAGTTCTATGTGAGGGACAAACTCTCATGACAGCAGCAGTGTTCTGGAATCACTTGTGAGGGCCAAACACTCAGACTTATGCAGCAGTATTTACAGATCTTATGTGTGATGGAAAACACTCTGAACCCAGCAGCAGTGTTCTGGAATCCTATATGAGGAAAAACTCAGAACCTGCAGCAGTGTTCTGGAATCCTTAGTGAGGAGGTATTCAGAACCTCATATCAGTGTTATGGAATCGTATGTGAGGACAAACACTCTGAAACCAGCAGCAGTGTTCTGGAATCCCATGTGAGAGACAAACACGAGAATCCAGCAGCAGTATTCTGGAATCCTATGTGTGAAAACACCCAGAAACCAGCAGCGTAGTACTGGAAGGAAATCTTTGTTAGGGGCTAACATTCAGACACAAGCTGTATTCTGGAATCTATGTGAGGACAAACACTCCTATCAGTAGCAATGTTCTGCAATTCTTTAGCAGCAGACAACATCTTCAGGCCCTCATGCAGCAGTTTCAAAAATTCCACAAGAGTGAGAGATTAAACACTCCAGAACCCAGCAGAAATGCAGGGATCTATGTGAGGGCAAATACTTGGAATCCAGCAGCACTGTTCTTGAAACCTATGTGAGGGACAAGCACTCACAACAGCCACTGTGTACCAGAATCCTATTTGATTGTCAAACACTTCAGACCCTAGTAGAGGAGTGTTCTGGAATCCCTATGTGAAGGACAAACTCTAAATAACCAGCATAGCAGTGCTCTGGAATCTTTGGGAGAGAAAGCATCAGACCCTAGCAGTGTTCTGGGATCCTATGTGAGGGAAAAACATTCCAGACCCGCATAGCAGTGTTTGGAATCTATACGAGTGACAAACACTCAGAACCCACCAGCAGTGTTCTGAATCTTTTTGTGAGGTAAAAACACTCAGACCCTCAAAGCAGTGTTCTGGAATCCTGCGTGATGGAAAAACATTCAGACGTAGCTGTGTTCTGGAATCCTATGTGAGGGAGAAACATTGTGACCCTCATGTAGCATTGTTCTGGAATCCAATATGAGGGACAAACACTCAGAAGCCAGCAGCTGTATTCTGGAATGCCATATTGAGAAAAGACTCCAGAACCCAACAGCAGTGTTCTGGAGATCTATCAAGGAAATAACCCTAGAGATTGGAGCACTGTACTGGAAGTCTTATATTAGGGACACATATTCAGACACTCGTAGAAGTGTTCTGGAATACTATGTGAAAGGACAAACACTAAGAAAACAGCAGCAGGGCTTTGGAATCCTTTGTGAGGACAAAAAAACAGAACCCATCAGCAGTGTTCTGAGAATCATTGTGAGAAAAATGTTTCTAGGTCCTATTAACAGTGTTCTGGAGATCCTATGTGAGGTAAACATTCAGATCCCTCATAGCAGTGGTCTGGAATCGTATGTGAGAGACAAACCCTCACAACCCAGCAGCAGTGTTCTGCAATCCCTATGTGAGCGACGAACATTGAGAACTTCGTAGCAGTGTTCTGATATTCTATGTAGAGCAAACACTCACAACCCGGCAGCACTGCTCTGGAATCGTATGTGAGGACAACAACAGAACCCAGCAGCCGTGTTCTGGAAACCTCGTGAGGGACAAAATCTCAGAGCTCAGCAGCAGTGTTCTGCAATCCTATGTGAGTGACAAATACTCAGAACCCAGCAGCAGTGTTCTGGAATCTTTGTGAGGACAAACACTAGAACCCAGCAGCAGTGTTCTAGAGTCCTTTGTGAGGACAAACATTCAGAAACTCTCTTCCAGTGTTCTGGAATCTTAGGTGAGGGACAAACACACTGAACCCAGCAGCTGTTTTGGAATCCCATGTGAGGCAGAAACACTCAGAACTCAGCAGTGTTCTGGAATCTATGTGAGTGAAAAACACTCAGGAGCCAACAGCAGTGTTCACAGAATCTTTGTGGGCAAACCTTCAAGACCCTAGAATCAGTGTTCTGGAATCCTATGTGATGAACAAACACTCAGAACCCAACAGCAGTGTTTTTGATTCCTTTGTTTTGGAGAAACATTCAGACCATTGTAGCACTGTTCCACTATTCTATGTGAGGGACAAACTCTCAGAACCCAGTAGCAGTGCTAAGTCCTATGTGAGGACAAACACTCAGAACCCAGCAGCAGGGTTCTGGAATCCTATGTGAGGGTCAAGCACTCAGAGGCAGCAGCAGTGTTCTGGAATCCCTATGTGAGGGCTTACTAAGAACCCAGTCACTGTGTGCTGGAATCCTATGTGGGAGAAACATTAGAGACAGTCACTGTGTGCTGGAATCCTATCTCAAGGACAAACATTCAGACCATTGTAGCACTGTTCCGCTATCCCTAGCGAGGGACAAACTCTCAGAACCCAGTAGCAGTGCTCTAGGAATCCTATGTGAGGACAGAAACACTGAACCCAGCAGCAGCAGGAATACTGGAATCCTATGTGAGGTCAAACACTCAGAAGGCAGCAGCAGTATTCTGGAATACATGGCAGGAGAAACATTCAGAACCCAGTGCTGTGTGCTGGAATCCTATGTGAGGGGAGAAACACTCACAACTCAGTCACTATGTGCTGGAATCCTATCTGAGGACAAACATTCAGACATGTAGAAGTGTCCTGGAATCCTATGAGGGACAAACACTGAGAACCCAGCAGCAGAGTTCTAGAATTCTTCGTGAAGACAAACATTCAGACACTCGAAGCAGTGTCCTAGAATCTATGTGAGGACAAACACTTCTAGAACCCAGCAGAATTGTTCTGGAATCCTTTGTGATGGATGAGCATTTGAGCCCTCGTGGCAGTGTTCTGGAAACCTAAGTGAGGGCAAACACTCAGTTGTAGCAGTGTTCTGGAATCCTATGTGACTGACAAACACTCAGAACCCTGAAGCAATGTTATGAAATCCTGTGTGAGTGCAAACACTCAGAACCCACCATCAATGCTCTGCAATCCTATGTGAGGAAAGAAACACTCAGAAACCTGCAGCAGTGTTCTGGAATCTATATATGGGTCAATAATTCAGACCATCATAGCACTGTTCTGGAATGCTCTGTGAGGACAAACATTCAGAAACTTGTAGCAGAGTTCTGGAATCTATGTGAGGGAGAAACCCTCAGAACCTAGCAGTAGTGTTCTGGAATCCTTATGTGAGATAACACTCAAGACCAGCCGCAGTGTTCTGGAATGCTATGTGAGGACAAACACTCAAAACCAAGCAGCAGGATTCTGTTATCTACCATGAGACAAACACTCGAACCCAGCAGAACTGTTATGGAATCTATGTGAGGACAAACACTCACAAACAAGCAGCTTTTGGAATCCCTATGTGAGGAGAAATCTTCAGAACCTAGCAGCAGTGTTCTGGAATCGTATGTGTGGACTTCAGCACACTCAGAACCCAGCAGCATGTTGAGAATGCTATGTGAGGGAGAAACACACAAAACCCACCAGCAGTGTTCTGGTTTAATATATGCGGGACAAACACACAGAACCCAGCAGAAGTGTTCTGTAATCCCATGTGAGGGTCAAACACTCACAAACCAGCAGCAATGTTTTGGAGTCTCTTTGTGAGGGACAAACATTAAACCTCAATAAAGTGCTCTGCAATCTATCAGCGAGGAACAACACTCTACAGGCCCAGCAGCAATGTTTTCGAATCCCATGAAAGGGACAAACACTCAGAACTTCGGCAGCATTTTCTGGAATCCTATGGTGACAAACTCTCAGAACACAGCAGCGGTGTTCTAGAATCACTGTAGGAGACAAACATTCAGAATGATCATAACAGTGTTCTGGTATCTCATGTGAGGACAAACACTCGGAAACCAGCAGCAGTGCTCTGAATTCTTGCAGGACAAACAAACCGAAGAGGTTCTGGAATTACTGTAAAGGACCAAGCACTGAGAACCCAGGAGCAGCGTTCTGGAATCCCATGTGAGGGACAAACGCTCAGAACCCAACAGCAGTGTTCTGTAATCTAATTGAGGACAGACACTCACAGCCCAGCATTGTTCTAGATTCGCTGTGAGGAACCAAGCATTTCAGACCCTCGGCAGTGTTCTGGAATGTTATGTGAGGGACAACCCTCTGAACCCAGCAGGGTTCTGGAATCAGTGAGTGACAAACACTCAAAACCCAGCAGCAGTGTTCCGGAATCCTTTGTGAGGACAAGCTTTCCAAACCTCGAAGCATTGTTATGGAGTCACCTTAGCAACGAGGAACACACTCAGAATCCCGCGCGCAGCGATATGATCTTGTGATGGACAAACATCCAGACACTCTTAGCAGTGTTCTGGAACGCTATGTGATGATTGTAAACCTACAGGCCAGGCAGTGTTCTGGAATCCTCTGTGAGGACAAACACTCAGAACCCAGTAGTAGTGTTCTGGAATCTAATGCATGAGGACAAACACACTAAGAACCCAAGGAGCAGTGTTCTGCAATCTATGAGGGACAAACACTACAGCCCACCAGCATGGCAGTGTTCTAGAATCCTTTGTGAGGAAAAACATTCAGACCATCGAATCAGTGTTCTGGAATCTATATGTGGGGAGACAAACGCTCAGAACCCAGCAGCAGTTTTCTGATCCTTTTCAGACAGACAAACCTTTAGACGATCTTAGCAGTGTTCTGTTATCTATGTAAGGGACAAACACTCAGAACCCAGCAGCAGTGCTCTGGATTCCTTTGTGGGGACGAGCACTTAGAACCCAGGAGCAGTGTTCTGGAATCCTATGTGAGGACAAACACTCAGAATCCAGCAGCAGTGTTCTGGAATCTTAGAGTGAGGACAGACACTCACAACCCAGCAGCAGTGTTCTAGAATCCTTTGTGAGGGACAAACAGCATCAGACCACAGAAGCAGTGTTTCTGGAATCTATGTGAGAGCAAACACTCAGAGACACAGCATCAGTGTTTCACAGAATCCTATCTTGAGTGACAAACTAGAACCAGAACAGTATTCATCCATTGTAGAGGACAAACATTCTGTCTCAGCGAAGCATTTTTCTGGATTCCTATGCTGAGGGACACACTCAGAACCCAGCAGCAGTGTTCTGGAATCCTATGTGTGGGACAAACACTCAGAAACCAGCAGCAGTGTTCTGGAATCCTACCGTGAGGGACAAACACTCAGAACACAGCTACTCTGTACTGGGAATCTATCTGAGTATTGACAACATTCAGACTCTTGCAGAAGTGTTCTGGAATCCTATGTGATGGACAAACACTAACAAACTAGCAGCAGCGCTCTGGAATTCTTTGTGATACAGACGTGTTCAAGGAGCTCTTTAACAGTGTTCTGGAATCGTATGTGAGTACAAACACTCAAAACTCAGCAGCAGTGTTCTGGAATTCTATTTGAGGACAAACTCTCAGAACCCAGCAGCCATGCTGTGAAATGATATGTGGACAGACACTCAGAACCCAACAGCAGAGTTCTGGTATCTAAGTGAGGAACAAACACTCAGAACCCTGCAGAAGTATTCTGGAATCATGTGAGGGACAAACACTCAAAATCCAAGAAGGCAGTGTTCTGGAATCCTATGTGAGGACAAACACTCACACCCTCGAAGTGTTCTGGAATCTATGTGAAGGACAAACACTCAGAACCCAGTAGCAGTGTTCTGGAATCTGGTGTGAAGGACAAGCGTTCAGACTTGCTCGTAGCAGTGATATGGAGTTGCTGTAGAGACAAGCATTCCAGACACACTTATGTTCTGGAATCCTAAGTGAGAGAAACCCTCAAAAACAAGCTGCAGTGTTCTAGGAAATCTATGAAAGGACAATCCCTCAGTATCGAGGCAGTGTTTGGAATCCTATCTGAGGGACAAACACTCAGAACTCAGCAGCAGTGTTCTGGAATCCTGTGTGAAGGAGAAACACTAGAACCCAACAGCAGTGTTCTGATTCCCGAAGTGTGGGACAATCACTCAAAACCCAGCCACTGTGTTCTGGAATCCTATCTGAGGTCAATGTAGGAACCTCGAGGAAGAGTTCTGGAATCCTATGTGAGGGAAAACACTCTGAAACCAGCAGAAGTGTTCTGGAATCCTTTGTGAGGGACAAACACTGAGAAATCAGAGCCGTGTTCTGGCATCCTATGTAGCGACAAACACTCTGAACCCAGCAGCAGTGTTTTGAATCACGTGAGCGACAAACACTCAGAACCCAAAGCAGTGTTCTGGAATACTTTTTGAGGACAATCATTCAGAACCTTGTAGCTGTGTTTCTGGAATCATATGTGAGGGCCAGCGAACACTTTGAACCCAGCTGCAGTGTTTTTGATTCCCCTGTGAAGGGAAAAACACTCAGGGCAGCAGCAGTGTTCTAGAATCAGCGTAATGGGACTAACATTCAGACCCTCAACGGTAACTTTTGGTCTATGTGAGGGACAAACACTGAGAACCCAACTGCAGTATTCTGCAATCCTTTGTGACAGAGAAACACTCAGACCATCGTAGCAGTGTTCTGGCATCCTATGTGCAGGAAAAACACTCCAAGAAACCAGCATCAGTGCTCTGGATTCCTTTGTGAGGGACAAACAAACAGAACCAGCAGCAGAGTTCTGGAATCCTATGTTGAGGACAAACACTCCAGAACCCATCAGCAGTGGTCAGAAATAATTTGAGGACAAACATTCAGAACCTAGTAGCAGTGTTCTGGAATAGTATGTGAGGACAAACACTCTAGGCAAACTGGCAGTCTTTTGGAATCACACGTGAGGGACAAAAACTCCAGAACCAAGCAGCAATGTTCTGAATACCATGTGAGAGACAACACTCAGAGCCCAGCAGCAGTGTTCTGGAATCTTATTTGAGTGACAAACACTGAGCTTAGCAGCAGAGTATTTACAGAGTCCTTTATGAGAACAAACTTCAGACACGCAGTCTTAAGATCCTATGTGAGAGACAAACCCTCAGAACCTTGAAGCAATGTTCTGCAATCCTTTTTGTTGGACAAACATTCCAGACCCTCGTAGCAGTGTTCCAGAATCCTATGTGGCGAAGGAACAAACACTCAGAACCCAGCAGTAGTGTTCGGGAATCCTATGGGAGGGACAACCATTTCCAGATCCAGCAGCAGTGTTGTGTAGTCTGTGAGGACAAACACTTTCAGAACCCAGCAGCTGTGTTCTGAAACCTATGTGAGGAAAATCATGAACCCAGCGTGTTGTGTTCTGGAATCCTATCTGAGGGAGAAATATTCAAACACTGTAGAAGAGTTCTGGAATCCTATGTGAGGGAAAAACCCTCAGAAGCCAGCAGTGCTCTGGAATCCTTTGAGCAAACAAATCAGAACCCTAGAAGCAGTGTTCTTGGATCTTTCCAGCTAGGAAAAACAGCTTCAAGACCCTCATAATAGTATTTTGGAATCCTATCTGAGGGACAACACTCAGACCAGCAGCTGTGTTCTGGAATCCTATATTATTAAGATAAACACTTAGAACCCAGCACAATATTCTGGAATACTACGTGAGCGACAAACTTTCAGAAGTTTGTAGCAGTATTCTACAGAATTCTATGTGAGGGACAAACACACAAGGCCAACAACTTGATAAGTGGTTCCTAAGTGAGGACAAACATTCAGAACCCAGCAGCAGTGTTCTGGTATCCTATGTGAGGACAAACACTCAGAACCCAGCAGCAGTGTTCTACAGAAATCCCTTTGTGAAGAGAAAAATGGCAGACCCTGCGCAGTGTTCTACTGGAATCCTATGTGATAGAAAAGTTCATACCCTCATAGCAGTGTTCTGGGATCCTATATGAGGTTGGCTTACAGAACCCACCAGCAGCGCTCGGAAACCACACTCTCTAGTGTTCTTGAATCCCATGTGAGAGAAACCTTCATACCCTCGTAGCATTGTTCTGGAATCAATATGAGGACAAACACTCAGAACCAGCCCAACATTCTGGAACCTTTATTGAGGATAAACATTCAGACCGTCATAGCAGTGTGCTGGAATCCTATGTGAGGGACAAATGCTCGAACCCAGCAGCAGTGGACTGGAGTCCTATGTGAGGACAGTACTCTGAGCTTAGCAGCAGTGTTCTGGAATCCTCTGTGAGGGACAAACTTTCACAACTGGCAGTGTTCTGGAGGCTTGTGAGTACAAACATTCAGAACCCAGCAGTGTTCTGGAAGTCCTTTGTGAGAACATTGTTGGAACCTCATAGCAATGTTCAGGGAGTAGGCGTACGTAAGGGACAAACACTCAGGAACACAGCAGCAGTGTTCTGCAATCCCATATGGACAAACACTCGAACCCAGCTGCAATGTTCTGTAATCCCTGTTTGACGACAAAGGCTCAGAAACCAGCAGCACTGTTCAAGAATCCTTTTTTGTGTGACAAACATTCTGAACCTCTAAAAGCAGTGTTCTGGAATCCTACTGTGAGGACAAACACCACAATCCCTGCAGCAGTTTTCTGGAATCCTTTGTGATGGACAAACATATTCAGACCCTCGTAGCAGTTTTCAGAATCCTATGTGTGGGACAAACACTCAGAACACAGCAACAGTGGTCTAGAATCCTTTGTGTGGGACAAAGATTCAGAACCCAGCAGCAGTGTTCTGGAATCCTATCAGGTACAAACACTCAGAAACAGTACAGCTTGTACTTTTGGATTCCACTGTGTACTGGAATCCTATCTGAAGGAAAAACATTCCGAACTTCGTAGAAGTTTTGGAATCCTGTGTGACGGACAAACACTAGAAATCTGCAGCAGTGTTCTAGAATCCTTTCTGAGTGACAAACAAACAGAACCCAGGAGCAGTGTGCTGCTATCCTTTTGAGGAAAAACTTTCACATCCTTATAGCAGTGTTCTGAAACCTATGTGAGGAAAGAAATTCAGACCCTCGTAGCAGTGCTCTGGAATCCTATATGAGGACAAACACTCAGAACCCAGCAGCAGTCTTCTGGAATCCTTTGGAGGAAAAACATTCACACCCTCGTAAAAGTGTTCTGGAATCTGTGAAGGAAAACATTCAGACCCTCGTAGCATTGTTCTGGAATCTAATATGAGGACAAACAGTCAGAACCCAGTTGCAGTGTTCTGGAATACTATGTGAGTGACAACACTCAGAACCCAGGAACTGGGTTCTGGAATTGTCTGTGCGGGCCAGTCATTCAGAACCTCATTATGATATTTCTGAGTCTATGTGAGGGAAAAACACTGTGATCTCAGCAGCAGTGTTCTGGAATCTATGTGAGGGCGAAACCTCTGACCAGCAGTCGTGTTCTGGAATCCCATGTGAGACAAACACTGAGATCTAGCAGCCTGTTCTGAATCCTATGTGAGTACAAACTCTCAGAACCCAGCAGCAGTGTTATGGAGTCCTTTGTGAGAGACAAACATTCAGACCCTCGTAGCAGTGTTCTGGAATCTTGTGAGGCACAAACACTCACAGCAGTAGACCCTCGTAGGAGTGTTCTGGAATCTACGTAAGGGACAAACACTCAGAACTCAGTGATTATTTTCTTGAAAGCTAAGTGAGTACAAACACTCGAAACCAGCAGTGTTCTGGGAATCTTGGTGAGGACTAACACTCCAGAACCCAACAGCATGTTCTGGGAGTATATGTGAAACAAGAACTCAAGAACTCAAACAGTGTTCTGGAATCGTATGTGAGGAACAAGCAATCAGGGCCAGCAGCAGCAGCCATGGAATCCTATGTGAGGGACAAACACTCAAACCCAGCCACTGTGTTCTGGAAACCTATCTAGTGATGACAAACATTCAGACACTCGTGGAAGTGTTCTGGAATCCTCGTGAGAGGCGGCTCAGAAACCAGCATAGGTGTTCTGGAATCCTTTTTGTGGAGAAACAAACAGAACCCAGCAGCAGTCTTCTGGAATCTATGTGAGGGAAAATATTTAGAACCCCGTAGCAGTGAAATACCTGGAATTCTATGAGGACACAACACACAGGACCCAGCAGCAGTGTTCTGGAACCTTATGTGATGGACAAACACTGAGAACACAACAGCAGTGTTCTGAAATCACATGTCAGCAGAAAAACATTCAGAAATTCATAGCAGTGTTCTGGAATCCTTTGTGACAGACAACACTCAGACTGTCGTAGCAGTGTTCTGATTTCCCATGAGAACAAACACAGCTAACATGTCTCAAAATCTCATGGGATCTATGCAAGGAACAACACAAGAGCACCCACACTATGTTCTTAAATACTAAAGAAACAACTTATTCAAACACTGGCCAAAGTATTCTAGAATCTATGTGAGGATAAACACTCAGAAACCAGCAGCAGTATTCTGGAATCCTTTGTGAGGGAAAAACATTAGACTCACGCATTCTTTAAAAATCTCTGTGTGAGGGACAAACCGTCTGAACTGAGCAGCAGTGTTCTGCAATCACTCTTGAGAGACAAACACTCACAGACAGCAGCAGTGTTCTGAAATCTAAATGAGGAACAAACCCTCAGAGACAGCAGCAGTGTTCTGAGTCCTTGTGGGGTACAACATTCAGAACCTCGAAGCAGTGTTCTGGAATCTATTTGAGGACAAACTCACAGAACCCAGCAGCAGTATTCTGGAATCCCAAGTGAGGGACAAACACTCAGAAACCAGCAGCAGTGTGCTGGAATGCTTTGAGGACAACATTCAGACCTTCGAAGCAGTGTTCTGCAATCCTATGTGATTGACAACTCTCAGAACCTAGGAGCAATCTTCTGTAATCTGTTGTGATGGAGAAACATTCGGAACCTCTTCGCCAGTGTTCTGGAATCTAGGTGTGGGAGAAACACTCAGAATCCAGCAGCAATGTTGGAAGTCTCTGTGAGAAAACACTCAAGGCTCAGCAGCGTAGTGTTCTGGAATCCTATGTGACCAGACAAACACTCAGATCACTGCAGCAGGGGGTCTGAAATCCTATGTGAAGGATAAGCACTCAGAACCCAGGAGCAGCGTTCTGGAATCCTTTCTGAGGACAAACATTCAGAACCTCGTAACAGTGTTCTGGAATCTTATGTGAGGACAAACACTCAGAACCCAACTTGGCAGCATTGTTCTGGAATCTTAGATGTGGGACAAACACTCCAGAACCAGGCATTAACAGTTCTGGAGTCCCATGTGAGGACAAACACTCAGAACCCAACAGCAGTATTCTGGAATCCTATGTGAGTGACAAACACTCAGAATCCAGCAGCAGTGTTCTAGAATTCTTTGTGTGGGACAAGCTTCATGCCCTCAAAGCAGTACTCTGGAATCCTATGTGAGGGAGGAACAGTCACAACCCAGCAGCAGTGTTCAGGAATCCTTTGTGACTGGACAAACATTCAGACCGTCGGAGCAGTGTTCTGGAATCTAAGTGAGGACAAACTACTCAGAACCAAGCCACTGTGTTCTGGAATCCTTCTGAGGGACAAATATTCAGACACCGTGAGTGTTCTGGAATCTATGTGAGGACAAACACTCAGAAAACAGCAGCAGTGCTATGGAGACCTTTGTGAGGAGCAGCAAACACAGCCAGAGTTTTATTCTGTAACCTTTTTGAGAGAAAACATTCAGAACCCCGTAGCAGTGTTCTGGAATCTATGTAGGGGACAAACATTCAGAACCCAGCAGCCGTGTTTTGGAATCCTGAGTGAAGACAAAGATTCAGAACTTCATAGCACTGTTCTGGAATCCCAGCTGAGACAGAAACACTCAGAACCCAGCAGTGTTCTAGAATCTATGTGAAGACAAACCCTCAGAACCCAACAGCAGTGTTCTGGAATCCATGTGAGGGACAAACACTCAGTACCCAACCACTGTGTTCTGGAATCCTATATGAAAAGGGACAAACATTCAGACAATCGTAGAAGTGTTCTGGAATCCTATATGAGGACAACACTCAGAAACCACCAGCAGTGCTCTGGAATCTTTTGTGAGGACAAAAATCTGAACCCAGCAGCACTCATTATTCTCTAATCATTTTAGGGACAAACGTTCAGAACCTCGTAGGAGGTTCTTGAATCTAAGTGAGGATAAAGCCCAGGCAGCAGCAGTGTTCTGGAATCTGCGTGAGTGACAAACACTCCGAACCCCGCAGGAATGTTCTTGAATCCTTTGTGAGGGACAAACATTCAAACCCTCGAAGCTATGGTGCTATGGAATCTATACATGAGGTACAAACAGTCATAACCCAGCAGAAATCTTCTGGAATCCTTGTTATGGACAAACATTGAGCCCTTGTAGCAGTGTTACGATCTAATGGAGGCACAAACACTCAGAACCCAGCAGCAGTGTTCTGGAATCTTATGTGAGGGACAAACACTGCAATCCAGCAGAAGTGTTCTGGAATCCTATCTGAGGACATACACTCAGAACCCAGTAGCAGTATTCTGGAATTCTATGTGATGGTACACGCTCAGAAACCAACAGCTGTTTTCTGGAATCTTGTCCAGTGACAAATATTCAGACACTCGTGGAAGTGTTCTGGAATCCTATGTGAGGGATAAACACTCAGAAACTAGCAGCGGTGATCTGGAATCCTTTGTAGAGGCTCAACAGAACCCAGCAGCTGTGTTCTGGAATCTTTGTGAGGAAAAATATTTAGACCCTTGTAGCAGTGTTCTGGAATCTATGTGAGGGACAAACACTGATACAACCCAGCGGCAGTGTTCTGGACTCCTCTATGAAGTCAAACCCTCAGAACCCAGCAGCAGTTTTCTGAAATAAAATGTGAGCAACAAACATTCAGAATTTCGTAGCAGAGTTCTGGAATCCTAGCGAGTGACAAACACTCAGGGAAACCAGCAGCAGTGTTCTAGAATCCTTTCTGTGGGACAAACTTTCAGACGCTCAAAGCAGTGTTCTGGAATCCTATGTGATGGACAAACACTCCGATCCCATCAGCAATGTTCTGCAATCCTTTGTGATGGGCAAACATTCAGACCCTCGTAACAGATTTTGGAATCTAAGTGAGGGACAAACACTCCAGAACCCAGCAGCAAGCAGTGTTCTAGAATCCTATATGAAGAACAAACACTCACAACCCAGCAGCCAGTATTGCTAATCTGTTTGAGGGACAAACACTCCAGAACCCACTCACTGTGTACAGGAATCCTATCTACCATGGGCTAACACATTCAGACCCTCGTAGCAGTGTTCTGGAATCCTATGTGAGGAGAAACTCTAAAAAACCAACAGCAGTGCTCTGGAATCCTTTATGAGGGAAAACATTCAGACCTTTAGCAGTGTTCTGGAATCCTATGTGAGGGAAATATTTTCAGAGCCTCATAGCAATGTTTCTTAATCATATATGAGTGACAAACGCCAGAAACCAGCAGCAGTGTTCTGGAATCCCTTGAGAGGGAAAAACATTTACACCTTCATAACAGTGTTCTGGAATCCTTACTGTGGGAAAAATATTCAGACCCTCGTAACAGTGTTCTGGAATCCTATATGAGGGACAAACACTCAAAACCAGCAGCAGTGTTCTGGAATCTATAGCCAGAGAAGCGTACTCAGAGCTGTACAGTGTTCTGGAGTCTATGGAGTGACAAACTTTTGAAATTCGCTGGCAGTATTCTGGAATCTTATGTGAGGACAAACACACAGAACCCAGTAGCAGTGTTCTGGAATCTTATGTGAGTAACAAACACTCAGAATCCAGCAACAGTGTTCTGGAATCCTATGTGAGGACAAACACTCCAGAACTAGCAGCAGTGTTCTAGGAATACTTTGTGAGGAAAAACACTCAGAACACAGTAGTGTTCTGGTATCCACTATTATTATAGAATCCTATCTGAGACAAACATTCAGAACCTAATAGTAGAAATGTTGCAATTCTACGTGAGGGACAAATACTAAGAAATCTGCAGCAGTGCTCTGGAATCTATTGTGAAGGTCAAACAAATAGAACCCAGTAGCCTTGTTCTACAATACTTTATGAGGAAAAACTTTCAGACCCTCATGGTGGTCTGGAATCACACGTAGGAACAAACACTCAGAGACAGCAGCAGTGTTCTGTACTCCTTTGTGAGGACAACATTCAGTTCCTCAGAGCAGTATTTGGAATCCTATGCTTTGAATGACAAGCACTAAGAAACCATCAACAGTGTTCTGGAATCTATGCTGAATGACAAACCTAAGAAACCATCAGCAGTGTTCTGGAATCCTTTGTGAGTAGCTAAACATTCGACCCCCTTAGCAGGGTTCTGGAACTATGTGAGGACATTCAGACACTTAGCAGTGTTTTGGCGCCTTAGCAGTGTTTGGAAACCAATGTGAGGGCCAAACAGTCAGAACCCAGCATCAGTGTTCTGGAATACTTGGTAAGGGACAAGCATTCAGAAAATCTTATCAGTTTTCTGGAATCCCAACTGAGGAGAAACGCTCCAGAAAATATCTGCAGTGTTCTAGAATTCTATGTGAGGACAAACCCTCATTGCGAGCTGCAGTGTTCTGGATTCCCTAGGTGAGGGACAAACACTCCAGAACAAAGCAGCAGTGTTCACAGTCTCATAACGATGGACAAAAACTCAGAACCCAGCAGTGTTCTGATACCTATGGGAGGGACAAACACTCAGAACCCAGCCCCTGTGTTCTGGAATCCTATCTGAAGGACAAACATTCGGAGACTTGAAGAAGTTTTCTGGAATCTATGTGAAGGACAAACAGTCAGAAACCTGTAGCAATGTTCTGGAATCATTTGCAGGAACAAACACTCAAAACTCAAAAGCAGTATCCTGGAATCCTACGTGAGGCCCAAGCCTAAGAACCCAGCAGCAGTATTTTCGAATCCTTAATGAGTGACAAACAGTCCAGAAACTTGCAACATTATTTTAGGTTGCTGTCTCTAGTACAGAGTTCTGGCCAAGAACAAACGCCAGAACAACCACTGTATTTCACAGAATATTGCTCTGAGAAAAAATAGCCGAGCCTCGTAGAAATTATTTCACAGAATCCCTATGGTAACCAAATACTCGAAAACCGCTCAACAGTGCTCTGGAATCCTTTGTGATGGATAAATAAACAGAGCCCAGCAGCAGTGTTCTGGAATCCTTCGTGAGGACAAACATTCAGAACCTTGTAGCCGTGTTCTGGAATCGTATGTGAAGGGTCAAACACTTTGAACCAGCAGCTGTGTTCTGGAATCTCTATGTGAGGGACAGAAGCACTAGAACCCAGCAACAGTGTTCTGTAATCCTTACTAGTAGAGGACAAAGCACAAGAGCCTTAGCATTGTTCTGCAATCCTTTGTGTGGGGACAAAACACTCAGGCCCAGCAGCAGAGTTGAATCCCATGTGAGGGACAAACGTTCAGGCACTCAGAATAGTGTTTGGAATCCTATGTTAGGGACAAACACTCAGAAAACTGCAGCAGTGTTCTGGAATCACACGTGGGGATGTGACTGAATCCTGATAGCACTGTTGTGGAATGCTCTGTGAGGAACAAACAATCAGACCCTCATCAGCAGTGTTCACAATCCTATGTAAGTACAAACCCTCACAACTCAACTAACTTTCTGGAATTCTATGCGAGGACAAACTCAGAACCTAACAACTTGTTCTGGAATCATACGTAAGGTAATAACACTCAGAACCCTGCAGCAGTGTTCTGGAATGCTATGTAAGAGACAAACACAAAACAGAGCAGTAGTATTCTGGTATCCTATATGAGGTAAAAACACTCAGAGACAACAGAAGTGTTCTGAAATCTATGTCAGGCACAAACATTTAGAGCTCCCAGAAGTGTTCTGGAATATTATGTGAAGGACAAAAACTCAGAATCAGGTGCAGTATTCTGGAATCCTATGTGAGGGACAAACATTCAGACCCTCCTAGCAAGTGTTCTGGAATGCAATCTGTTGTAAAAACCCTCAGAACACAGAAGCAGTTGTCTGGAATCCTTTGTGATGAAGAAACTATTCCAGACCCTAGTAGCAGTGTTCTGGAATCTATGTGACGGACAAACCTTCAGAATCCAGCAATAGTGTACTGGAATCCTCTGTGAGGACATACACTCAGAACCCAGCAGTAGTGTTTTGGAATCCTTTGTGAGGACAAACCCTCAGAATCAGCAGTAGTGTTCTGGAATCCTCTGTGAGGGCCATACCCTCAGAACCAACCCGGTATTGTTCTGGAATCCTATGTCAGGAGGACAAACATTGAAACCAGCAGTTTTCTGGAATCCTATGTGAGGACAAACACTCAGAAACCAGCAGCAGTGTTCTACTGCAATCCCTATGTGAGGACAAACACTCTGGAAACCCAGCAGCAGTGTTCTAGAATCCTATGTGATGACAAACATTCAGAATTTTGTAGCAATGTTCTGCCATTCCATGTGAGTGACAAACACTCAGAAACCAGCAACAGCCTTCTAGAATCTATCGCAAGGAAAAACACTCAGAAGCCAGCAACAATGTTCTAGCATCCCTTGTGAGGGACAAACATTCAGAATCTCGTAGAAGTGCTCTGGAATCGCAAGTGAGGGAGAAACACACAGGCCCAGCAGCCCAATGTTTTGGAATCCTGTTTGAGCGACAAAGATACAGAACTCGTTGCAATGTTCTGGAATCCCATGTGAGGGACAAACACTGTGAGAATCCCAGCAGCAGTGTCTATGAGCTTATTACAGCTTACACATTTTTGTTACCCTTTTGCGCATTTTTATGTGCACACACACCAACCCACCCACCCACTTACACTATGTGAACAAACACTCAGAACCCAGCAGTGTTCTACAATCTATGTGAGGACAAACATTCAAGCTCATGTAGTGTTCTGCAATCCCTGTGTGAGGACAAACACTCAGAACCCAGCCACTGTGTTCTGGAATCTATCTGAGGACAAACATTCAGACACTTGGCAGAAGTGTTCACAGAATCCTATGAGGGTAAACACTCAGAAACAAGCAGCGGTGCTCTGGAGATGCCACAGAGGGACAAACAGAGCCCAGCAGTGTCCTGGAATCGAGGAAAATGGTGAGACCCTCGTCTCAGTTTTTACAATCCTATGTGAGGGAGAAACACTCAGAACTGGCAACAGTGTTCTAGAATCCATGTGAGAGACAAACACTGAGTTCTAGCAGCCCTGTTCTGGAATCCTATGTGAGTACAAACTCAGACACTCACGAAGCAGTGTTTGGGATCCCTATGTGAGGACCGGTCAGAACCTTGGCAGTCTTCTGATTCCCTAGAGTGGCTGTTCCGACCCTCGCTTGAGGATTCTGGAATCTATGTGAGGACAAACGCCAGAACCTACCCCTTAGTATTACAGAATCTTGAACAATACTCAAGGCGCGCAGGGTC', ) - expect(r1?.get('cigar')).toEqual(r2?.get('cigar')) - expect(r1?.get('cigar')).toBe( + expect(r1?.CIGAR).toEqual(r2?.CIGAR) + expect(r1?.CIGAR).toBe( '48M4D36M1D97M5D14M1D5M1D37M2D44M1D5M1I11M2I3M2D6M2I8M1D45M3D43M1D4M2D41M1D58M1D31M2D7M1D31M5I3M1D24M2D1M1D19M1D8M1D16M2D25M1I11M1I14M2I7M1D10M2I1M1I4M1I8M1I8M1I18M2D7M1D8M1D64M2D38M1I17M2I13M1I32M2I16M1D11M1D6M1D5M3D41M1I20M1D6M1D47M1I72M4D50M1I71M1I5M3D8M1I25M1I2M1D5M1D4M1I20M1D3M2D10M1I57M1I49M1D34M1I12M2D6M1I5M1I24M1I14M2D11M1I71M1I55M1D48M1D9M2D30M1D100M1D46M1D24M1I49M2D39M3D17M1D41M1I6M1D10M3D8M1I161M2D3M1D12M1D62M1D23M1I12M5D1M2I37M2D12M1D3M1I1M2D68M1I4M1D39M1I13M1D4M2I7M2D14M2I2M1I2M1I16M1D40M1D3M1D25M1D24M1I48M1D17M2D23M2D89M1D8M1D11M2I84M1D14M2D2M2D75M1D49M1I37M1D56M1D38M1D47M1I9M2D2M1D8M1I3M2D30M1D38M1D3M1I16M1D25M1D8M1D28M4D6M1I9M1D47M1D5M3I1M1I26M1D149M1I20M2D7M1I3M1D14M1D4M2I20M2I49M1I9M1D17M3D40M1I1M2D20M1I33M1D39M4D18M2D3M1D2M1D11M2D3M1I8M1I83M1D8M1D18M3D18M1I1M2D9M1I6M1I12M2D29M1D13M3D18M3D53M1D38M2I6M3I6M2D17M1I12M1D1M1D3M2D56M3I1M1D11M2D5M2D24M1D44M2I3M1D6M2I13M1I20M3D19M1D3M3I4M2I26M1D39M1I11M1I32M2D2M1I48M1D54M1D49M1D42M1I5M1D59M2I18M1I9M1D8M1D15M1I14M1I3M1I11M1I14M3D4M1D3M1D11M4D9M1I2M1D18M1I26M1I6M2D86M1I39M1I14M3I95M2D6M2I5M2I3M1D3M1I27M1D47M1D45M3D38M1D48M2D26M1I4M1I24M1D20M1D2M2D13M1D73M2I23M1I1M2D3M1D13M1I12M4D18M2D35M1I10M1D23M2D7M1D77M1D83M1D4M1D3M1D41M1D64M1D25M1D31M1D8M2D27M1D27M1D29M1I22M3I45M1I14M2D23M2I1M3D2M1I22M1D3M1D4M2I5M1D120M2I52M1D42M1I31M2D3M1D47M1D59M1I22M1D18M1D57M2D14M1I3M2I16M1D6M1D6M2D14M2D71M1I35M4I59M1I30M3D5M1D10M2I23M1D13M1D9M2D1M1D7M2I2M1D44M1D46M3D21M2D3M3D6M1I11M1I24M2I4M1D9M2I3M1I40M1D10M2D28M2I83M2I25M2D4M1I9M1D5M2I4M1D11M1D47M1D35M3I3M1I12M1I6M1D10M1I1M3D8M3I23M2D41M2I1M4D26M1D15M4D23M2D37M1D8M1D16M1D4M2I5M3D18M1D59M1D35M1D4M1D61M2D1M2D12M1D5M1D5M1D18M3D16M1I11M5D5M2I23M1I5M3I23M1I32M3D12M1D25M1I9M1D40M1I28M2I23M1I4M1D56M2I19M1D110M2D25M2I4M1D5M3I63M2D27M1D82M1D33M1D13M1D47M1D43M1D3M1D39M3D8M1D44M1D115M3I6M1D1M1D4M1D4M1D47M1D17M1D6M2D28M2D17M1D7M1D8M1D13M1D88M2D20M8D6M80D26M1D31M1I4M1D20M1D12M1D5M3D12M1I5M1D8M1D11M1I15M1D31M1I8M1D2M1D38M1D14M1I62M3I3M1D41M1D10M1I39M1D38M1D11M1D26M3I1M1I12M2D3M1D5M1I92M1I93M3D8M5D8M4D12M39D2M1I6M1D13M1D8M1I6M2D22M3D6M1D3M2I30M1D8M1D59M1D3M2D4M1D4M3D6M3I4M1I69M2D1M1I23M1D24M1I1M2D15M1D6M1D11M1D33M1D8M1D88M2D5M1D4M1D114M1I14M1D41M2D13M2D2M1D19M2I24M1I27M1I69M1D47M1D20M5I39M1I17M1I19M1D104M1D86M1I39M1D8M1D8M1I56M1D4M1D2M1D12M1D8M1D49M1I11M1D68M1D55M1D67M3D17M1D8M1D38M1D55M3I49M1D46M1D26M4I11M1D35M1D10M1D8M1D4M1D9M3D21M1D82M1I1M2I12M1D4M2I45M1D20M1D20M2D2M1D68M1D35M1D49M1D138M1I7M5D37M1D38M1D23M2I123M1D18M2I163M1D5M1D20M1I67M1I5M1I2M2D3M1D20M1I34M3I5M1D3M2I41M1D50M1D16M2D56M1I4M1D24M1D145M1D25M1D4M1I19M5D5M2I14M1D4M1D15M1D9M1I26M1D95M1D11M1I5M1D17M1I31M3D24M1D2M2I16M2D17M3I12M2D111M1D22M3D18M1D19M1I1M2D29M1D30M1D12M3I42M1D5M1I12M1D40M1I11M1D24M2D8M1D13M2I14M1I1M1I10M1D113M1D11M1I36M1D15M1D22M1I21M1I21M1I10M1D23M3D16M1D96M1D53M1D59M1D50M1I29M2D3M18D8M1D11M2I2M8D2M3D8M1D5M2D10M1I4M1I9M1I6M1D9M1D18M2I4M1I6M1I6M3D4M1I16M1I76M1D46M1I40M1I14M1I2M1I4M1D30M2I1M1I2M1I2M1D7M1I3M1D7M1I3M3D23M1I5M1I10M1D16M3D43M1D67M3D3M1I6M1D56M1I10M2D1M1I10M1D22M2D25M1D7M2D16M1D76M2D55M1I1M2D20M1D23M1D50M1D55M1I74M1I4M1I3M1I27M1D56M1D47M1D17M1D50M1I28M2I11M2D5M3D26M1D31M3I7M1I9M1D14M2I33M1D86M1D119M1D9M2I41M1D40M2I7M1I13M1D2M1I3M4I3M73I6M3D18M3D17M1D8M1D12M2D8M1D15M1I9M1D38M1D8M1D20M1I12M1I10M2D4M1D35M1I2M1I2M2D20M3D18M6D1M1D7M1I1M2D22M1D32M1D21M1D23M1D32M1D7M2D10M2I12M1D6M1I10M4D17M2D10M1D6M3D2M1D6M2D2M1I30M1D8M1D10M1D11M46S', ) - expect(r1?.id()).toEqual(r2?.id()) + expect(r1?.id).toEqual(r2?.id) }) test('pair across chrom', async () => { @@ -306,11 +304,11 @@ test('long read consistent IDs', async () => { const [r1, r2] = [ret1, ret2].map(x => x.find( k => - k.get('name') === + k.name === 'm131004_105332_42213_c100572142530000001823103304021442_s1_p0/103296', ), ) - expect(r1?.id()).toEqual(r2?.id()) + expect(r1?.id).toEqual(r2?.id) }) test('long read consistent IDs chm1 pacbio', async () => { @@ -323,11 +321,11 @@ test('long read consistent IDs chm1 pacbio', async () => { const [r1, r2] = [ret1, ret2].map(x => x.find( k => - k.get('name') === + k.name === 'm131009_195631_42213_c100579462550000001823095604021430_s1_p0/145814', ), ) - expect(r1?.id()).toEqual(r2?.id()) + expect(r1?.id).toEqual(r2?.id) }) test('long read consistent IDs hg002 nanopore', async () => { @@ -336,9 +334,9 @@ test('long read consistent IDs hg002 nanopore', async () => { const ret1 = await ti.getRecordsForRange('1', 200000, 700000) const ret2 = await ti.getRecordsForRange('1', 700000, 900000) const [r1, r2] = [ret1, ret2].map(x => - x.find(k => k.get('name') === '901e456a-b7cf-4624-bd27-e2981a6c7ca5'), + x.find(k => k.name === '901e456a-b7cf-4624-bd27-e2981a6c7ca5'), ) - expect(r1?.id()).toEqual(r2?.id()) + expect(r1?.id).toEqual(r2?.id) }) test('long read consistent IDs hg002 nanopore 2', async () => { @@ -347,17 +345,16 @@ test('long read consistent IDs hg002 nanopore 2', async () => { const ret3 = await ti.getRecordsForRange('1', 200000, 560000) const ret4 = await ti.getRecordsForRange('1', 500000, 700000) const [r3, r4] = [ret3, ret4].map(x => - x.find(k => k.get('name') === '7c318bae-cae9-4cf9-8efc-c761304aa0da'), + x.find(k => k.name === '7c318bae-cae9-4cf9-8efc-c761304aa0da'), ) - expect(r3?.id()).toEqual(r4?.id()) + expect(r3?.id).toEqual(r4?.id) }) test('long tag list', async () => { const ti = new BamFile({ bamPath: 'test/data/long_tag_list.bam' }) await ti.getHeader() const ret1 = await ti.getRecordsForRange('1', 0, 3000000) - expect(ret1[0]._tags().includes('SB')).toBeTruthy() - expect(ret1[0]._tags()).toMatchSnapshot() + expect(ret1[0].tags).toMatchSnapshot() }) test('fix decoding error for ID tag', async () => { @@ -365,22 +362,22 @@ test('fix decoding error for ID tag', async () => { await ti1.getHeader() const ret1 = await ti1.getRecordsForRange('1', 0, 3000000) - expect(ret1[0].get('ID')).toBe(78190) - expect(ret1[1].get('ID')).toBe(4440) + expect(ret1[0].tags.ID).toBe(78190) + expect(ret1[1].tags.ID).toBe(4440) }) test('fix decoding error for DI tag', async () => { const ti1 = new BamFile({ bamPath: 'test/data/long_tag_list2.bam' }) await ti1.getHeader() const ret1 = await ti1.getRecordsForRange('1', 0, 3000000) - expect(ret1[0].get('DI')).toBe(78190) - expect(ret1[1].get('DI')).toBe(4440) + expect(ret1[0].tags.DI).toBe(78190) + expect(ret1[1].tags.DI).toBe(4440) }) test('get CIGAR from a CG long tag', async () => { const ti1 = new BamFile({ bamPath: 'test/data/cg.bam' }) await ti1.getHeader() const ret1 = await ti1.getRecordsForRange('chr1', 0, 3000000) - expect(ret1[0].get('CIGAR').slice(0, 4)).toBe('1M1D') + expect(ret1[0].CIGAR.slice(0, 4)).toBe('1M1D') }) test('get header text', async () => { diff --git a/test/csi.test.ts b/test/csi.test.ts index 4de50e9..5526d8a 100644 --- a/test/csi.test.ts +++ b/test/csi.test.ts @@ -82,6 +82,6 @@ test('SAM spec pdf', async () => { const features = await b.getRecordsForRange('ref', 1, 100) expect(features.length).toEqual(6) - expect(features[2].get('sa')).toEqual('ref,29,-,6H5M,17,0;') - expect(features[4].get('sa')).toEqual('ref,9,+,5S6M,30,1;') + expect(features[2].tags.SA).toEqual('ref,29,-,6H5M,17,0;') + expect(features[4].tags.SA).toEqual('ref,9,+,5S6M,30,1;') }) diff --git a/test/fakerecord.ts b/test/fakerecord.ts index 8f3cdb2..e6e90ba 100644 --- a/test/fakerecord.ts +++ b/test/fakerecord.ts @@ -9,6 +9,8 @@ export default class FakeRecord extends Record { start: 0, byteArray: Buffer.from([ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, ]), }, }) @@ -17,7 +19,8 @@ export default class FakeRecord extends Record { this.strand1 = strand1 === 'R' this.strand2 = strand2 === 'R' this.tlen = tlen - this._refID = 1 + this.nextrefid = 1 + this.refid = 1 } isRead1() { @@ -36,11 +39,15 @@ export default class FakeRecord extends Record { return this.strand1 } - template_length() { + get template_length() { return this.tlen } - _next_refid() { - return 1 + get next_refid() { + return this.nextrefid + } + + get ref_id() { + return this.refid } } diff --git a/test/vanilla-node.test.ts b/test/vanilla-node.test.ts index 1973d0c..6765c8b 100644 --- a/test/vanilla-node.test.ts +++ b/test/vanilla-node.test.ts @@ -28,15 +28,15 @@ test('gets features from volvox-sorted.bam', async () => { await ti.getHeader() const records = await ti.getRecordsForRange('ctgA', 0, 1000) expect(records.length).toEqual(131) - expect(records[0].get('start')).toEqual(2) - expect(records[0].get('end')).toEqual(102) - expect(records[0].get('cigar')).toEqual('100M') - expect(records[0].get('name')).toEqual('ctgA_3_555_0:0:0_2:0:0_102d') - expect(records[0].get('qual')).toEqual( + expect(records[0].start).toEqual(2) + expect(records[0].end).toEqual(102) + expect(records[0].CIGAR).toEqual('100M') + expect(records[0].name).toEqual('ctgA_3_555_0:0:0_2:0:0_102d') + expect(records[0].qual).toEqual( '17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17', ) - expect(records[0].get('md')).toEqual('100') - expect(records[0].getReadBases()).toEqual( + expect(records[0].tags.MD).toEqual('100') + expect(records[0].seq).toEqual( 'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG', ) await bam.close() diff --git a/yarn.lock b/yarn.lock index e3c73b5..5e934ce 100644 --- a/yarn.lock +++ b/yarn.lock @@ -11,48 +11,38 @@ "@jridgewell/trace-mapping" "^0.3.24" "@babel/code-frame@^7.0.0", "@babel/code-frame@^7.22.13": - version "7.24.7" - resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.24.7.tgz#882fd9e09e8ee324e496bd040401c6f046ef4465" - integrity sha512-BcYH1CVJBO9tvyIZ2jVeXgSIMvGZ2FDRvDdOIVQyuklNKSsx+eppDEBq/g47Ayw+RqNFE+URvOShmf+f/qwAlA== + version "7.26.2" + resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.26.2.tgz#4b5fab97d33338eff916235055f0ebc21e573a85" + integrity sha512-RJlIHRueQgwWitWgF8OdFYGZX328Ax5BCemNGlqHfplnRT9ESi8JkFlvaVYbS+UubVY6dpv87Fs2u5M29iNFVQ== dependencies: - "@babel/highlight" "^7.24.7" + "@babel/helper-validator-identifier" "^7.25.9" + js-tokens "^4.0.0" picocolors "^1.0.0" 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deep-eql@^5.0.1: version "5.0.2" @@ -899,10 +927,10 @@ eastasianwidth@^0.2.0: resolved "https://registry.yarnpkg.com/eastasianwidth/-/eastasianwidth-0.2.0.tgz#696ce2ec0aa0e6ea93a397ffcf24aa7840c827cb" integrity sha512-I88TYZWc9XiYHRQ4/3c5rjjfgkjhLyW2luGIheGERbNQ6OY7yTybanSpDXZa8y7VUP9YmDcYa+eyq4ca7iLqWA== -electron-to-chromium@^1.5.4: - version "1.5.13" - resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.5.13.tgz#1abf0410c5344b2b829b7247e031f02810d442e6" - integrity sha512-lbBcvtIJ4J6sS4tb5TLp1b4LyfCdMkwStzXPyAgVgTRAsep4bvrAGaBOP7ZJtQMNJpSQ9SqG4brWOroNaQtm7Q== +electron-to-chromium@^1.5.41: + version "1.5.52" + resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.5.52.tgz#2bed832c95a56a195504f918150e548474687da8" + integrity sha512-xtoijJTZ+qeucLBDNztDOuQBE1ksqjvNjvqFoST3nGC7fSpqJ+X6BdTBaY5BHG+IhWWmpc6b/KfpeuEDupEPOQ== emoji-regex@^8.0.0: version "8.0.0" @@ -960,7 +988,7 @@ esbuild@^0.21.3: "@esbuild/win32-ia32" "0.21.5" "@esbuild/win32-x64" "0.21.5" -escalade@^3.1.2: +escalade@^3.2.0: version "3.2.0" resolved "https://registry.yarnpkg.com/escalade/-/escalade-3.2.0.tgz#011a3f69856ba189dffa7dc8fcce99d2a87903e5" integrity sha512-WUj2qlxaQtO4g6Pq5c29GTcWGDyd8itL8zTlipgECz3JesAiiOKotd8JU6otB3PACgG6xkJUyVhboMS+bje/jA== @@ -988,18 +1016,18 @@ eslint-plugin-prettier@^5.1.3: prettier-linter-helpers "^1.0.0" synckit "^0.9.1" -eslint-plugin-unicorn@^55.0.0: - version "55.0.0" - resolved "https://registry.yarnpkg.com/eslint-plugin-unicorn/-/eslint-plugin-unicorn-55.0.0.tgz#e2aeb397914799895702480970e7d148df5bcc7b" - integrity sha512-n3AKiVpY2/uDcGrS3+QsYDkjPfaOrNrsfQxU9nt5nitd9KuvVXrfAvgCO9DYPSfap+Gqjw9EOrXIsBp5tlHZjA== +eslint-plugin-unicorn@^56.0.0: + version "56.0.0" + resolved "https://registry.yarnpkg.com/eslint-plugin-unicorn/-/eslint-plugin-unicorn-56.0.0.tgz#9fd3ebe6f478571734541fa745026b743175b59e" + integrity 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"@eslint/plugin-kit" "^0.2.0" + "@humanfs/node" "^0.16.6" "@humanwhocodes/module-importer" "^1.0.1" - "@humanwhocodes/retry" "^0.3.0" - "@nodelib/fs.walk" "^1.2.8" + "@humanwhocodes/retry" "^0.4.0" + "@types/estree" "^1.0.6" + "@types/json-schema" "^7.0.15" ajv "^6.12.4" chalk "^4.0.0" cross-spawn "^7.0.2" debug "^4.3.2" escape-string-regexp "^4.0.0" - eslint-scope "^8.0.2" - eslint-visitor-keys "^4.0.0" - espree "^10.1.0" + eslint-scope "^8.2.0" + eslint-visitor-keys "^4.2.0" + espree "^10.3.0" esquery "^1.5.0" esutils "^2.0.2" fast-deep-equal "^3.1.3" @@ -1058,26 +1090,23 @@ eslint@^9.9.0: ignore "^5.2.0" imurmurhash "^0.1.4" is-glob "^4.0.0" - is-path-inside "^3.0.3" json-stable-stringify-without-jsonify "^1.0.1" - levn "^0.4.1" lodash.merge "^4.6.2" minimatch "^3.1.2" natural-compare "^1.4.0" optionator "^0.9.3" - strip-ansi "^6.0.1" text-table "^0.2.0" -espree@^10.0.1, espree@^10.1.0: - version "10.1.0" - resolved 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version "3.1.3" @@ -1234,16 +1253,6 @@ generic-filehandle@^3.0.0: dependencies: es6-promisify "^6.1.1" -get-func-name@^2.0.1: - version "2.0.2" - resolved "https://registry.yarnpkg.com/get-func-name/-/get-func-name-2.0.2.tgz#0d7cf20cd13fda808669ffa88f4ffc7a3943fc41" - integrity sha512-8vXOvuE167CtIc3OyItco7N/dpRtBbYOsPsXCz7X/PMnlGjYjSGuZJgM1Y7mmew7BKf9BqvLX2tnOVy1BBUsxQ== - -get-stream@^8.0.1: - version "8.0.1" - resolved "https://registry.yarnpkg.com/get-stream/-/get-stream-8.0.1.tgz#def9dfd71742cd7754a7761ed43749a27d02eca2" - integrity sha512-VaUJspBffn/LMCJVoMvSAdmscJyS1auj5Zulnn5UoYcY531UWmdwhRWkcGKnGU93m5HSXP9LP2usOryrBtQowA== - git-raw-commits@^5.0.0: version "5.0.0" resolved "https://registry.yarnpkg.com/git-raw-commits/-/git-raw-commits-5.0.0.tgz#38af4301e70c17be03fec01a37a6cd90ce0db04e" @@ -1303,10 +1312,10 @@ globals@^14.0.0: resolved "https://registry.yarnpkg.com/globals/-/globals-14.0.0.tgz#898d7413c29babcf6bafe56fcadded858ada724e" integrity sha512-oahGvuMGQlPw/ivIYBjVSrWAfWLBeku5tpPE2fOPLi+WHffIWbuh2tCjhyQhTBPMf5E9jDEH4FOmTYgYwbKwtQ== -globals@^15.7.0: - version "15.9.0" - resolved "https://registry.yarnpkg.com/globals/-/globals-15.9.0.tgz#e9de01771091ffbc37db5714dab484f9f69ff399" - integrity sha512-SmSKyLLKFbSr6rptvP8izbyxJL4ILwqO9Jg23UA0sDlGlu58V59D1//I3vlc0KJphVdUR7vMjHIplYnzBxorQA== +globals@^15.9.0: + version "15.12.0" + resolved "https://registry.yarnpkg.com/globals/-/globals-15.12.0.tgz#1811872883ad8f41055b61457a130221297de5b5" + integrity sha512-1+gLErljJFhbOVyaetcwJiJ4+eLe45S2E7P5UiZ9xGfeq3ATQf5DOv9G7MH3gGbKQLkzmNh2DxfZwLdw+j6oTQ== graphemer@^1.4.0: version "1.4.0" @@ -1325,11 +1334,6 @@ handlebars@^4.7.7: optionalDependencies: uglify-js "^3.1.4" -has-flag@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/has-flag/-/has-flag-3.0.0.tgz#b5d454dc2199ae225699f3467e5a07f3b955bafd" - integrity sha512-sKJf1+ceQBr4SMkvQnBDNDtf4TXpVhVGateu0t918bl30FnbE2m4vNLX+VWe/dpjlb+HugGYzW7uQXH98HPEYw== - has-flag@^4.0.0: version "4.0.0" resolved "https://registry.yarnpkg.com/has-flag/-/has-flag-4.0.0.tgz#944771fd9c81c81265c4d6941860da06bb59479b" @@ -1359,10 +1363,10 @@ html-escaper@^2.0.0: resolved "https://registry.yarnpkg.com/html-escaper/-/html-escaper-2.0.2.tgz#dfd60027da36a36dfcbe236262c00a5822681453" integrity sha512-H2iMtd0I4Mt5eYiapRdIDjp+XzelXQ0tFE4JS7YFwFevXXMmOp9myNrUvCg0D6ws8iqkRPBfKHgbwig1SmlLfg== -human-signals@^5.0.0: - version "5.0.0" - resolved "https://registry.yarnpkg.com/human-signals/-/human-signals-5.0.0.tgz#42665a284f9ae0dade3ba41ebc37eb4b852f3a28" - integrity sha512-AXcZb6vzzrFAUE61HnN4mpLqd/cSIwNQjtNWR0euPm6y0iqx3G4gOXaIDdtdDwZmhwe82LA6+zinmW4UBWVePQ== +ieee754@^1.2.1: + version "1.2.1" + resolved "https://registry.yarnpkg.com/ieee754/-/ieee754-1.2.1.tgz#8eb7a10a63fff25d15a57b001586d177d1b0d352" + integrity sha512-dcyqhDvX1C46lXZcVqCpK+FtMRQVdIMN6/Df5js2zouUsqG7I6sFxitIC+7KYK29KdXOLHdu9zL4sFnoVQnqaA== ignore@^5.2.0, ignore@^5.3.1: version "5.3.2" @@ -1438,16 +1442,6 @@ is-obj@^2.0.0: resolved "https://registry.yarnpkg.com/is-obj/-/is-obj-2.0.0.tgz#473fb05d973705e3fd9620545018ca8e22ef4982" integrity sha512-drqDG3cbczxxEJRoOXcOjtdp1J/lyp1mNn0xaznRs8+muBhgQcrnbspox5X5fOw0HnMnbfDzvnEMEtqDEJEo8w== -is-path-inside@^3.0.3: - version "3.0.3" - resolved "https://registry.yarnpkg.com/is-path-inside/-/is-path-inside-3.0.3.tgz#d231362e53a07ff2b0e0ea7fed049161ffd16283" - integrity sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ== - -is-stream@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/is-stream/-/is-stream-3.0.0.tgz#e6bfd7aa6bef69f4f472ce9bb681e3e57b4319ac" - integrity sha512-LnQR4bZ9IADDRSkvpqMGvt/tEJWclzklNgSw48V5EAaAeDd6qGvN8ei6k5p0tvxSR171VmGyHuTiAOfxAbr8kA== - isexe@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/isexe/-/isexe-2.0.0.tgz#e8fbf374dc556ff8947a10dcb0572d633f2cfa10" @@ -1494,13 +1488,11 @@ jackspeak@^3.1.2: "@pkgjs/parseargs" "^0.11.0" jackspeak@^4.0.1: - version "4.0.1" - resolved "https://registry.yarnpkg.com/jackspeak/-/jackspeak-4.0.1.tgz#9fca4ce961af6083e259c376e9e3541431f5287b" - integrity sha512-cub8rahkh0Q/bw1+GxP7aeSe29hHHn2V4m29nnDlvCdlgU+3UGxkZp7Z53jLUdpX3jdTO0nJZUDl3xvbWc2Xog== + version "4.0.2" + resolved "https://registry.yarnpkg.com/jackspeak/-/jackspeak-4.0.2.tgz#11f9468a3730c6ff6f56823a820d7e3be9bef015" + integrity sha512-bZsjR/iRjl1Nk1UkjGpAzLNfQtzuijhn2g+pbZb98HQ1Gk8vM9hfbxeMBP+M2/UUdwj0RqGG3mlvk2MsAqwvEw== dependencies: "@isaacs/cliui" "^8.0.2" - optionalDependencies: - "@pkgjs/parseargs" "^0.11.0" js-tokens@^4.0.0: version "4.0.0" @@ -1588,12 +1580,10 @@ long@^4.0.0: resolved "https://registry.yarnpkg.com/long/-/long-4.0.0.tgz#9a7b71cfb7d361a194ea555241c92f7468d5bf28" integrity sha512-XsP+KhQif4bjX1kbuSiySJFNAehNxgLb6hPRGJ9QsUr8ajHkuXGdrHmFUTUUXhDwVX2R5bY4JNZEwbUiMhV+MA== -loupe@^3.1.0, loupe@^3.1.1: - version "3.1.1" - resolved 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version "11.0.2" + resolved "https://registry.yarnpkg.com/lru-cache/-/lru-cache-11.0.2.tgz#fbd8e7cf8211f5e7e5d91905c415a3f55755ca39" + integrity sha512-123qHRfJBmo2jXDbo/a5YOQrJoHF/GNQTLzQ5+IdK5pWpceK17yRc6ozlWd25FxvGKQbIUs91fDFkXmDHTKcyA== -magic-string@^0.30.10: - version "0.30.11" - resolved "https://registry.yarnpkg.com/magic-string/-/magic-string-0.30.11.tgz#301a6f93b3e8c2cb13ac1a7a673492c0dfd12954" - integrity sha512-+Wri9p0QHMy+545hKww7YAu5NyzF8iomPL/RQazugQ9+Ez4Ic3mERMd8ZTX5rfK944j+560ZJi8iAwgak1Ac7A== +magic-string@^0.30.12: + version "0.30.12" + resolved "https://registry.yarnpkg.com/magic-string/-/magic-string-0.30.12.tgz#9eb11c9d072b9bcb4940a5b2c2e1a217e4ee1a60" + integrity sha512-Ea8I3sQMVXr8JhN4z+H/d8zwo+tYDgHE9+5G4Wnrwhs0gaK9fXTKx0Tw5Xwsd/bCPTTZNRAdpyzvoeORe9LYpw== dependencies: "@jridgewell/sourcemap-codec" "^1.5.0" -magicast@^0.3.4: +magicast@^0.3.5: version "0.3.5" resolved "https://registry.yarnpkg.com/magicast/-/magicast-0.3.5.tgz#8301c3c7d66704a0771eb1bad74274f0ec036739" integrity sha512-L0WhttDl+2BOsybvEOLK7fW3UA0OQ0IQ2d6Zl2x/a6vVRs3bAY0ECOSHHeL5jD+SbOpOCUEi0y1DgHEn9Qn1AQ== @@ -1633,11 +1623,6 @@ meow@^13.0.0: resolved "https://registry.yarnpkg.com/meow/-/meow-13.2.0.tgz#6b7d63f913f984063b3cc261b6e8800c4cd3474f" integrity sha512-pxQJQzB6djGPXh08dacEloMFopsOqGVRKFPYvPOt9XDZ1HasbgDZA74CJGreSU4G3Ak7EFJGoiH2auq+yXISgA== -merge-stream@^2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/merge-stream/-/merge-stream-2.0.0.tgz#52823629a14dd00c9770fb6ad47dc6310f2c1f60" - integrity sha512-abv/qOcuPfk3URPfDzmZU1LKmuw8kT+0nIHvKrKgFrwifol/doWcdA4ZqsWQ8ENrFKkd67Mfpo/LovbIUsbt3w== - merge2@^1.3.0: version "1.4.1" resolved "https://registry.yarnpkg.com/merge2/-/merge2-1.4.1.tgz#4368892f885e907455a6fd7dc55c0c9d404990ae" @@ -1651,11 +1636,6 @@ micromatch@^4.0.4: braces "^3.0.3" picomatch "^2.3.1" -mimic-fn@^4.0.0: - version "4.0.0" - resolved 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+1762,9 @@ p-try@^2.0.0: integrity sha512-R4nPAVTAU0B9D35/Gk3uJf/7XYbQcyohSKdvAxIRSNghFl4e71hVoGnBNQz9cWaXxO2I10KTC+3jMdvvoKw6dQ== package-json-from-dist@^1.0.0: - version "1.0.0" - resolved "https://registry.yarnpkg.com/package-json-from-dist/-/package-json-from-dist-1.0.0.tgz#e501cd3094b278495eb4258d4c9f6d5ac3019f00" - integrity sha512-dATvCeZN/8wQsGywez1mzHtTlP22H8OEfPrVMLNr4/eGa+ijtLn/6M5f0dY8UKNrC2O9UCU6SSoG3qRKnt7STw== + version "1.0.1" + resolved "https://registry.yarnpkg.com/package-json-from-dist/-/package-json-from-dist-1.0.1.tgz#4f1471a010827a86f94cfd9b0727e36d267de505" + integrity sha512-UEZIS3/by4OC8vL3P2dTXRETpebLI2NiI5vIrjaD/5UtrkFX/tNbwjTSRAGC/+7CAo2pIcBaRgWmcBBHcsaCIw== pako@^1.0.11: version "1.0.11" @@ -1841,11 +1807,6 @@ path-key@^3.1.0: resolved "https://registry.yarnpkg.com/path-key/-/path-key-3.1.1.tgz#581f6ade658cbba65a0d3380de7753295054f375" integrity sha512-ojmeN0qd+y0jszEtoY48r0Peq5dwMEkIlCOu6Q5f41lfkswXuKtYrhgoTpLnyIcHm24Uhqx+5Tqm2InSwLhE6Q== -path-key@^4.0.0: - version "4.0.0" - resolved "https://registry.yarnpkg.com/path-key/-/path-key-4.0.0.tgz#295588dc3aee64154f877adb9d780b81c554bf18" - integrity sha512-haREypq7xkM7ErfgIyA0z+Bj4AGKlMSdlQE2jvJo6huWD1EdkKYV+G/T4nq0YEF2vgTT8kqMFKo1uHn950r4SQ== - path-parse@^1.0.7: version "1.0.7" resolved "https://registry.yarnpkg.com/path-parse/-/path-parse-1.0.7.tgz#fbc114b60ca42b30d9daf5858e4bd68bbedb6735" @@ -1877,10 +1838,10 @@ pathval@^2.0.0: resolved "https://registry.yarnpkg.com/pathval/-/pathval-2.0.0.tgz#7e2550b422601d4f6b8e26f1301bc8f15a741a25" integrity sha512-vE7JKRyES09KiunauX7nd2Q9/L7lhok4smP9RZTDeD4MVs72Dp2qNFVz39Nz5a0FVEW0BJR6C0DYrq6unoziZA== -picocolors@^1.0.0, picocolors@^1.0.1: - version "1.0.1" - resolved "https://registry.yarnpkg.com/picocolors/-/picocolors-1.0.1.tgz#a8ad579b571952f0e5d25892de5445bcfe25aaa1" - integrity sha512-anP1Z8qwhkbmu7MFP5iTt+wQKXgwzf7zTyGlcdzabySa9vd0Xt392U0rVmz9poOaBj0uHJKyyo9/upk0HrEQew== +picocolors@^1.0.0, picocolors@^1.1.0: + version 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sha512-56rxCq7G/XfB4EkXq9Egn5GCqugWvDFjafDOThIdMBsI15iqPqR5r15TfSr1YPYeEI19YeaXMCbY6u88Y76GLQ== dependencies: nanoid "^3.3.7" - picocolors "^1.0.1" - source-map-js "^1.2.0" + picocolors "^1.1.0" + source-map-js "^1.2.1" prelude-ls@^1.2.1: version "1.2.1" @@ -2012,28 +1973,30 @@ rimraf@^6.0.1: package-json-from-dist "^1.0.0" rollup@^4.20.0: - version "4.21.2" - resolved "https://registry.yarnpkg.com/rollup/-/rollup-4.21.2.tgz#f41f277a448d6264e923dd1ea179f0a926aaf9b7" - integrity sha512-e3TapAgYf9xjdLvKQCkQTnbTKd4a6jwlpQSJJFokHGaX2IVjoEqkIIhiQfqsi0cdwlOD+tQGuOd5AJkc5RngBw== + version "4.24.4" + resolved "https://registry.yarnpkg.com/rollup/-/rollup-4.24.4.tgz#fdc76918de02213c95447c9ffff5e35dddb1d058" + integrity sha512-vGorVWIsWfX3xbcyAS+I047kFKapHYivmkaT63Smj77XwvLSJos6M1xGqZnBPFQFBRZDOcG1QnYEIxAvTr/HjA== dependencies: - "@types/estree" "1.0.5" + "@types/estree" "1.0.6" optionalDependencies: - "@rollup/rollup-android-arm-eabi" "4.21.2" - "@rollup/rollup-android-arm64" "4.21.2" - "@rollup/rollup-darwin-arm64" "4.21.2" - "@rollup/rollup-darwin-x64" "4.21.2" - "@rollup/rollup-linux-arm-gnueabihf" "4.21.2" - "@rollup/rollup-linux-arm-musleabihf" "4.21.2" - "@rollup/rollup-linux-arm64-gnu" "4.21.2" - "@rollup/rollup-linux-arm64-musl" "4.21.2" - "@rollup/rollup-linux-powerpc64le-gnu" "4.21.2" - "@rollup/rollup-linux-riscv64-gnu" "4.21.2" - "@rollup/rollup-linux-s390x-gnu" "4.21.2" - "@rollup/rollup-linux-x64-gnu" "4.21.2" - "@rollup/rollup-linux-x64-musl" "4.21.2" - "@rollup/rollup-win32-arm64-msvc" "4.21.2" - "@rollup/rollup-win32-ia32-msvc" "4.21.2" - "@rollup/rollup-win32-x64-msvc" "4.21.2" + "@rollup/rollup-android-arm-eabi" "4.24.4" + "@rollup/rollup-android-arm64" "4.24.4" + "@rollup/rollup-darwin-arm64" "4.24.4" + "@rollup/rollup-darwin-x64" "4.24.4" + "@rollup/rollup-freebsd-arm64" "4.24.4" + "@rollup/rollup-freebsd-x64" "4.24.4" + "@rollup/rollup-linux-arm-gnueabihf" "4.24.4" + "@rollup/rollup-linux-arm-musleabihf" "4.24.4" + 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@@ -2297,23 +2248,23 @@ type-fest@^0.8.1: integrity sha512-4dbzIzqvjtgiM5rw1k5rEHtBANKmdudhGyBEajN01fEyhaAIhsoKNy6y7+IN93IfpFtwY9iqi7kD+xwKhQsNJA== type-fest@^4.6.0, type-fest@^4.7.1: - version "4.26.0" - resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-4.26.0.tgz#703f263af10c093cd6277d079e26b9e17d517c4b" - integrity sha512-OduNjVJsFbifKb57UqZ2EMP1i4u64Xwow3NYXUtBbD4vIwJdQd4+xl8YDou1dlm4DVrtwT/7Ky8z8WyCULVfxw== + version "4.26.1" + resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-4.26.1.tgz#a4a17fa314f976dd3e6d6675ef6c775c16d7955e" + integrity sha512-yOGpmOAL7CkKe/91I5O3gPICmJNLJ1G4zFYVAsRHg7M64biSnPtRj0WNQt++bRkjYOqjWXrhnUw1utzmVErAdg== typescript-eslint@^8.1.0: - version "8.3.0" - resolved "https://registry.yarnpkg.com/typescript-eslint/-/typescript-eslint-8.3.0.tgz#f4d9c5ba71f6bead03ec41ecb2bece1de511e49f" - integrity sha512-EvWjwWLwwKDIJuBjk2I6UkV8KEQcwZ0VM10nR1rIunRDIP67QJTZAHBXTX0HW/oI1H10YESF8yWie8fRQxjvFA== + version "8.13.0" + resolved 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uglify-js@^3.1.4: version "3.19.3" @@ -2330,13 +2281,13 @@ unicorn-magic@^0.1.0: resolved "https://registry.yarnpkg.com/unicorn-magic/-/unicorn-magic-0.1.0.tgz#1bb9a51c823aaf9d73a8bfcd3d1a23dde94b0ce4" integrity sha512-lRfVq8fE8gz6QMBuDM6a+LO3IAzTi05H6gCVaUpir2E1Rwpo4ZUog45KpNXKC/Mn3Yb9UDuHumeFTo9iV/D9FQ== -update-browserslist-db@^1.1.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/update-browserslist-db/-/update-browserslist-db-1.1.0.tgz#7ca61c0d8650766090728046e416a8cde682859e" - integrity sha512-EdRAaAyk2cUE1wOf2DkEhzxqOQvFOoRJFNS6NeyJ01Gp2beMRpBAINjM2iDXE3KCuKhwnvHIQCJm6ThL2Z+HzQ== +update-browserslist-db@^1.1.1: + version "1.1.1" + resolved "https://registry.yarnpkg.com/update-browserslist-db/-/update-browserslist-db-1.1.1.tgz#80846fba1d79e82547fb661f8d141e0945755fe5" + integrity sha512-R8UzCaa9Az+38REPiJ1tXlImTJXlVfgHZsglwBD/k6nj76ctsH1E3q4doGrukiLQd3sGQYu56r5+lo5r94l29A== dependencies: - escalade "^3.1.2" - picocolors "^1.0.1" + escalade "^3.2.0" + picocolors "^1.1.0" uri-js@^4.2.2: version "4.4.1" @@ -2353,51 +2304,51 @@ validate-npm-package-license@^3.0.1, validate-npm-package-license@^3.0.4: spdx-correct "^3.0.0" spdx-expression-parse "^3.0.0" -vite-node@2.0.5: - version "2.0.5" - resolved "https://registry.yarnpkg.com/vite-node/-/vite-node-2.0.5.tgz#36d909188fc6e3aba3da5fc095b3637d0d18e27b" - integrity sha512-LdsW4pxj0Ot69FAoXZ1yTnA9bjGohr2yNBU7QKRxpz8ITSkhuDl6h3zS/tvgz4qrNjeRnvrWeXQ8ZF7Um4W00Q== +vite-node@2.1.4: + version "2.1.4" + resolved "https://registry.yarnpkg.com/vite-node/-/vite-node-2.1.4.tgz#97ffb6de913fd8d42253afe441f9512e9dbdfd5c" + integrity sha512-kqa9v+oi4HwkG6g8ufRnb5AeplcRw8jUF6/7/Qz1qRQOXHImG8YnLbB+LLszENwFnoBl9xIf9nVdCFzNd7GQEg== dependencies: cac "^6.7.14" - debug "^4.3.5" + debug "^4.3.7" pathe "^1.1.2" - tinyrainbow "^1.2.0" vite "^5.0.0" vite@^5.0.0: - version "5.4.2" - resolved "https://registry.yarnpkg.com/vite/-/vite-5.4.2.tgz#8acb6ec4bfab823cdfc1cb2d6c53ed311bc4e47e" - integrity 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