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csi.ts
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csi.ts
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import { unzip } from '@gmod/bgzf-filehandle'
import VirtualOffset, { fromBytes } from './virtualOffset'
import Chunk from './chunk'
import {
optimizeChunks,
findFirstData,
parsePseudoBin,
parseNameBytes,
BaseOpts,
} from './util'
import IndexFile from './indexFile'
const CSI1_MAGIC = 21582659 // CSI\1
const CSI2_MAGIC = 38359875 // CSI\2
function lshift(num: number, bits: number) {
return num * 2 ** bits
}
function rshift(num: number, bits: number) {
return Math.floor(num / 2 ** bits)
}
export default class CSI extends IndexFile {
private maxBinNumber = 0
private depth = 0
private minShift = 0
public setupP?: ReturnType<CSI['_parse']>
async lineCount(refId: number, opts?: BaseOpts) {
const indexData = await this.parse(opts)
return indexData.indices[refId]?.stats?.lineCount || 0
}
async indexCov() {
return []
}
parseAuxData(bytes: Buffer, offset: number) {
const formatFlags = bytes.readInt32LE(offset)
const coordinateType =
formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'
const format = (
{ 0: 'generic', 1: 'SAM', 2: 'VCF' } as Record<number, string>
)[formatFlags & 0xf]
if (!format) {
throw new Error(`invalid Tabix preset format flags ${formatFlags}`)
}
const columnNumbers = {
ref: bytes.readInt32LE(offset + 4),
start: bytes.readInt32LE(offset + 8),
end: bytes.readInt32LE(offset + 12),
}
const metaValue = bytes.readInt32LE(offset + 16)
const metaChar = metaValue ? String.fromCharCode(metaValue) : ''
const skipLines = bytes.readInt32LE(offset + 20)
const nameSectionLength = bytes.readInt32LE(offset + 24)
return {
columnNumbers,
coordinateType,
metaValue,
metaChar,
skipLines,
format,
formatFlags,
...parseNameBytes(
bytes.subarray(offset + 28, offset + 28 + nameSectionLength),
this.renameRefSeq,
),
}
}
// fetch and parse the index
async _parse(opts: { signal?: AbortSignal }) {
const buffer = await this.filehandle.readFile(opts)
const bytes = await unzip(buffer)
let csiVersion
// check TBI magic numbers
if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
csiVersion = 1
} else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
csiVersion = 2
} else {
throw new Error('Not a CSI file')
// TODO: do we need to support big-endian CSI files?
}
this.minShift = bytes.readInt32LE(4)
this.depth = bytes.readInt32LE(8)
this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7
const auxLength = bytes.readInt32LE(12)
const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined
const refCount = bytes.readInt32LE(16 + auxLength)
type BinIndex = Record<string, Chunk[]>
// read the indexes for each reference sequence
let curr = 16 + auxLength + 4
let firstDataLine: VirtualOffset | undefined
const indices = new Array<{
binIndex: BinIndex
stats?: { lineCount: number }
}>(refCount)
for (let i = 0; i < refCount; i++) {
// the binning index
const binCount = bytes.readInt32LE(curr)
curr += 4
const binIndex: Record<string, Chunk[]> = {}
let stats // < provided by parsing a pseudo-bin, if present
for (let j = 0; j < binCount; j++) {
const bin = bytes.readUInt32LE(curr)
curr += 4
if (bin > this.maxBinNumber) {
stats = parsePseudoBin(bytes, curr + 28)
curr += 28 + 16
} else {
firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr))
curr += 8
const chunkCount = bytes.readInt32LE(curr)
curr += 4
const chunks = new Array<Chunk>(chunkCount)
for (let k = 0; k < chunkCount; k += 1) {
const u = fromBytes(bytes, curr)
curr += 8
const v = fromBytes(bytes, curr)
curr += 8
firstDataLine = findFirstData(firstDataLine, u)
chunks[k] = new Chunk(u, v, bin)
}
binIndex[bin] = chunks
}
}
indices[i] = { binIndex, stats }
}
return {
csiVersion,
firstDataLine,
indices,
refCount,
csi: true,
maxBlockSize: 1 << 16,
...aux,
}
}
async blocksForRange(
refId: number,
min: number,
max: number,
opts: BaseOpts = {},
) {
if (min < 0) {
min = 0
}
const indexData = await this.parse(opts)
const ba = indexData.indices[refId]
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
if (!ba) {
return []
}
const overlappingBins = this.reg2bins(min, max)
if (overlappingBins.length === 0) {
return []
}
const chunks = []
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
for (const [start, end] of overlappingBins) {
for (let bin = start; bin <= end; bin++) {
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
if (ba.binIndex[bin]) {
const binChunks = ba.binIndex[bin]
for (const c of binChunks) {
chunks.push(c)
}
}
}
}
return optimizeChunks(chunks, new VirtualOffset(0, 0))
}
/**
* calculate the list of bins that may overlap with region [beg,end)
* (zero-based half-open)
*/
reg2bins(beg: number, end: number) {
beg -= 1 // < convert to 1-based closed
if (beg < 1) {
beg = 1
}
if (end > 2 ** 50) {
end = 2 ** 34
} // 17 GiB ought to be enough for anybody
end -= 1
let l = 0
let t = 0
let s = this.minShift + this.depth * 3
const bins = []
for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {
const b = t + rshift(beg, s)
const e = t + rshift(end, s)
if (e - b + bins.length > this.maxBinNumber) {
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`,
)
}
bins.push([b, e] as const)
}
return bins
}
async parse(opts: BaseOpts = {}) {
if (!this.setupP) {
this.setupP = this._parse(opts).catch((e: unknown) => {
this.setupP = undefined
throw e
})
}
return this.setupP
}
async hasRefSeq(seqId: number, opts: BaseOpts = {}) {
const header = await this.parse(opts)
return !!header.indices[seqId]?.binIndex
}
}