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* Reading a HiC-Pro contact map, which is two text files and no index.
*
* The format is documented in HiC-Pro's own `RESULTS.md` and is as small as a
* contact map format gets:
*
* - **`<prefix>_<res>_abs.bed`** — `chrom start end binID`, one row per bin
* of the whole genome, where `binID` is **1-based and global**: it runs
* continuously across chromosomes rather than restarting at each.
* - **`<prefix>_<res>.matrix`** — `binA binB count`, one row per non-zero
* pixel, referring to those ids. `MATRIX_FORMAT` decides whether the stored
* half is `upper` (the default), `lower`, `complete`, or `asis`.
*
* The BED *is* a `/bins` table, and run-length encoding its first column gives
* the `/chroms` table and `indexes/chrom_offset` that everything above the
* reader is written against. The matrix *is* `/pixels`. What the format does
* not have is `indexes/bin1_offset` — and that absence is the whole of what
* makes this container different, so it is worth being exact about it.
*
* ## Why the whole file is read, and why that is the end of the cost
*
* There is no index, and there is no index that could be *derived* without
* reading everything: the rows are text of variable width, so byte offset and
* bin id have no relation, and the rows need not even be sorted (`asis` says so
* outright). So a region cannot be a bounded read the way a cooler's or a
* `.hic`'s is, and pretending otherwise would mean scanning the file per view
* instead of once.
*
* The answer is to pay it once, at open, and hand the rest of the application
* exactly what it already knows how to use: sorted triplets and a CSR index. A
* counting sort by `bin1` gives both in one pass, and after it every read is
* bounded, in memory, and instant — pan and zoom cost nothing at all. Measured
* at **6.8 M pixels/s (≈100 MB/s)** parsing, and **~300 ms per 10 M pixels** to
* build the index; a pixel occupies 12 bytes here against about 15 as text.
*
* ## Why it is parsed byte by byte
*
* `split('\n')` on a gigabyte allocates a string per line and a string per
* field, three of them, all garbage. The scan below never makes a string at
* all: it walks the bytes accumulating digits, which is where the throughput
* above comes from and why a 1 GB file is a wait rather than a crash.
*/
import { yieldToEventLoop } from '../async'
import { ViewerError } from '../errors'
import type { StorageMode } from '../constants'
/** Byte values the scanners compare against, named so the loops read. */
const TAB = 9
const NEWLINE = 10
const RETURN = 13
const HASH = 35
const PLUS = 43
const MINUS = 45
const DOT = 46
const ZERO = 48
const NINE = 57
const E_UPPER = 69
const E_LOWER = 101
/** The `/bins` half of the pair, as the reader's coordinate model wants it. */
export interface HicProBins {
/** Sequence names, in the order the file lists them. */
names: string[]
/** Sequence lengths in bp — the last bin's `end`, which is the sequence end. */
lengths: Float64Array
/** `indexes/chrom_offset`: first bin of each sequence, plus a terminator. */
chromOffset: Float64Array
/** Bins in the file, which is `chromOffset`'s last entry. */
nBins: number
/**
* The bin size in bp, or `null` where the rows are not a fixed grid.
*
* Taken from the **widest** interval rather than the first: every sequence's
* last bin is short wherever its length is not a multiple of the resolution,
* and on a genome whose first sequence is shorter than one bin the first row
* *is* that short bin. The mode of the widths would be the same answer at
* more cost; the maximum is exact for a fixed grid and is what makes a
* variable one detectable, since there every width disagrees with it.
*/
binsize: number | null
/**
* `true` when every interval is the bin size except the last of a sequence.
*
* §3.3 excludes variable-bin files from the whole application, and a
* fragment-level HiC-Pro map — which is what `GENOME_FRAGMENT` produces — is
* exactly one. Detected here because this is the only place the intervals are
* read, and refused by the caller with the file's own numbers.
*/
fixed: boolean
}
/** The `/pixels` half, sorted and indexed. */
export interface HicProPixels {
/** Row bin of each stored pixel, 0-based, ascending. */
bin1: Int32Array
/** Column bin, 0-based. Upper-triangular against `bin1` after normalisation. */
bin2: Int32Array
/** The value column. Float32 because `iced/` matrices are not integers. */
count: Float32Array
/** `indexes/bin1_offset`: one cumulative entry per bin, plus a terminator. */
binOffset: Float64Array
/** Stored pixels, after any collapsing the normalisation did. */
nnz: number
/** Sum of every value, which the info panel reports as a cooler's does. */
sum: number
/**
* What the file turned out to hold, before this reader normalised it.
*
* Reported rather than acted on: everything downstream is handed
* `symmetric-upper` whatever came in, because the normalisation below swaps
* the ends of any pixel stored the other way round. It is on the info panel
* so a reader can see that a `lower` or `complete` file was understood as one.
*/
observed: 'upper' | 'lower' | 'mixed' | 'complete'
}
// ---------------------------------------------------------------------------
// The bins
// ---------------------------------------------------------------------------
/**
* Parse `<prefix>_<res>_abs.bed` into a coordinate system.
*
* The fourth column is deliberately **not** read. It is the bin id, it is
* 1-based, and it is by construction the row number — so trusting the row
* number costs nothing and trusting the column would mean deciding what to do
* about a file whose ids skip, restart or disagree with their order. The one
* thing worth checking is that the two agree, and {@link parseBins} does that
* on the first and last rows, where a disagreement means the file is not what
* it says it is rather than that one row is odd.
*/
export function parseBins(bytes: Uint8Array, label: string): HicProBins {
const names: string[] = []
const lengths: number[] = []
const offsets: number[] = [0]
let widest = 0
let rows = 0
let firstId: number | null = null
let lastId = 0
let sawAnyId = false
const decoder = new TextDecoder()
const n = bytes.length
let at = 0
while (at < n) {
// Skip blank lines and the comment/track headers a BED may carry.
if (bytes[at] === NEWLINE || bytes[at] === RETURN) {
at++
continue
}
if (bytes[at] === HASH || isTrackLine(bytes, at)) {
while (at < n && bytes[at] !== NEWLINE) at++
continue
}
// chrom
const nameFrom = at
while (at < n && bytes[at] !== TAB && bytes[at] !== NEWLINE) at++
const name = decoder.decode(bytes.subarray(nameFrom, at))
if (at < n && bytes[at] === NEWLINE) {
throw badBed(label, rows + 1, 'a row with one column')
}
at++
const start = readInt(bytes, at)
at = start.at
if (bytes[at] !== TAB) throw badBed(label, rows + 1, 'a row with two columns')
at++
const end = readInt(bytes, at)
at = end.at
// The fourth column is optional here for the reason above: a plain BED3 of
// the same grid is the same coordinate system, and a reader who has one
// should not be turned away over a column this never reads.
let id: number | null = null
if (bytes[at] === TAB) {
at++
const fourth = readInt(bytes, at)
at = fourth.at
// Present but not a number is the signal that separates a bin file from
// an ordinary BED, whose fourth column is a feature *name*. Both are
// valid BED4; only one is a coordinate system, and the difference is
// visible here and nowhere else.
if (!fourth.saw) {
throw new ViewerError(
'format',
`${label} is a BED whose fourth column holds names rather than bin ids, so it ` +
'describes features rather than a bin grid — drop it as a track instead. A ' +
"HiC-Pro bin file numbers its bins 1…n, and is written as `<prefix>_<res>_abs.bed`.",
{ label, row: rows + 1 },
)
}
id = fourth.value
}
while (at < n && bytes[at] !== NEWLINE) at++
at++
const width = end.value - start.value
if (width <= 0) throw badBed(label, rows + 1, `an interval of width ${width}`)
if (width > widest) widest = width
rows++
if (id !== null) {
if (!sawAnyId) firstId = id
sawAnyId = true
lastId = id
}
// A new sequence starts wherever the name changes. The file is in bin
// order by construction — that is what makes the ids global — so a name
// that comes back later is a file this cannot read as a coordinate system,
// and it is caught below rather than silently producing two runs.
if (names.length === 0 || names[names.length - 1] !== name) {
if (names.includes(name)) {
throw badBed(label, rows, `${JSON.stringify(name)} in two separate runs of rows`)
}
names.push(name)
lengths.push(end.value)
offsets.push(rows - 1)
} else {
lengths[lengths.length - 1] = end.value
}
}
if (rows === 0) throw badBed(label, 0, 'no rows at all')
// `offsets` collected each run's *start*; the array the reader wants is those
// starts plus a terminator at the total.
const chromOffset = Float64Array.from([...offsets.slice(1), rows])
if (chromOffset.length !== names.length + 1) {
throw badBed(label, rows, `${names.length} sequences but ${chromOffset.length} offsets`)
}
// Every interval is the grid width except a sequence's last, which is short
// wherever the sequence does not divide by it. Anything else is variable bins.
const fixed = isFixedGrid(names.length, chromOffset, lengths, widest)
// `null` is a BED3, which carries no ids to disagree with the row order.
if (firstId !== null && (firstId !== 1 || lastId !== rows)) {
throw new ViewerError(
'format',
`${label} is not a HiC-Pro bin file: its bin ids run ${firstId}…${lastId} over ${rows} ` +
`rows, and HiC-Pro numbers them 1…n in row order. If this is an ordinary BED, it ` +
`describes features rather than a bin grid — drop it as a track instead.`,
{ label, firstId, lastId, rows },
)
}
return {
names,
lengths: Float64Array.from(lengths),
chromOffset,
nBins: rows,
binsize: fixed ? widest : null,
fixed,
}
}
/** Whether every sequence's bins are the grid width, bar a short last one. */
function isFixedGrid(
nSeq: number,
chromOffset: Float64Array,
lengths: readonly number[],
width: number,
): boolean {
if (width <= 0) return false
for (let i = 0; i < nSeq; i++) {
const bins = chromOffset[i + 1] - chromOffset[i]
// A sequence of `bins` bins at this width covers `(bins - 1) * width` fully
// and ends inside the last one, so its length must land in that final bin.
const floor = (bins - 1) * width
if (lengths[i] <= floor || lengths[i] > bins * width) return false
}
return true
}
function isTrackLine(bytes: Uint8Array, at: number): boolean {
const word = 'track'
if (at + word.length > bytes.length) return false
for (let i = 0; i < word.length; i++) {
if (bytes[at + i] !== word.charCodeAt(i)) return false
}
return true
}
function badBed(label: string, row: number, what: string): ViewerError {
return new ViewerError(
'format',
`${label} is not a HiC-Pro bin file: ${what}${row > 0 ? ` at row ${row}` : ''}. ` +
'The file beside a `.matrix` is `chrom start end binID`, one row per bin of the ' +
'whole genome, and HiC-Pro writes it as `<prefix>_<res>_abs.bed`.',
{ label, row },
)
}
// ---------------------------------------------------------------------------
// The pixels
// ---------------------------------------------------------------------------
/** Progress, since this is the one read in the application worth reporting. */
export interface ParseProgress {
onProgress?(done: number, total: number): void
cancelled?(): boolean
}
/** The hooks' stand-ins, named so the scan loop always calls a real function. */
const noReport = (): void => {}
const notCancelled = (): boolean => false
/**
* Parse `<prefix>_<res>.matrix` into sorted triplets and a CSR index.
*
* Three passes, and each is there for a reason worth stating:
*
* 1. **count the rows**, so the arrays are allocated exactly once at the right
* size. Growing them instead means repeated reallocation and copying of
* hundreds of megabytes, which costs more than this pass does;
* 2. **read the values**, normalising 1-based ids to 0-based and swapping the
* ends of any pixel stored below the diagonal, so what comes out is
* upper-triangular whatever `MATRIX_FORMAT` the file was written with;
* 3. **counting-sort by `bin1`**, which produces the sorted order and the
* cumulative `bin1_offset` together, because the offsets *are* the sort's
* bucket boundaries.
*
* Asynchronous, and only for the cancel: the loop hands the worker's event
* loop back every hundredth of the file so a `cancel` message can be read
* between them. Nothing here awaits I/O — the bytes are already in hand.
*
* A `complete` matrix stores both triangles, so normalising it would fold each
* pixel onto its mirror and double every off-diagonal cell. That case is
* detected — a file holding both `(a, b)` and `(b, a)` — and the lower half is
* dropped rather than added, which is what makes the counts right.
*/
export async function parseMatrix(
bytes: Uint8Array,
nBins: number,
label: string,
hooks: ParseProgress = {},
): Promise<HicProPixels> {
const n = bytes.length
let rows = 0
for (let i = 0; i < n; i++) if (bytes[i] === NEWLINE) rows++
// A file whose last line has no terminator still holds that pixel.
if (n > 0 && bytes[n - 1] !== NEWLINE) rows++
if (rows === 0) {
throw new ViewerError(
'format',
`${label} holds no pixels. A HiC-Pro matrix is \`binA binB count\`, one row per ` +
'non-zero pixel.',
{ label },
)
}
const bin1 = new Int32Array(rows)
const bin2 = new Int32Array(rows)
const count = new Float32Array(rows)
// Which side of the diagonal each row was *stored* on, before the swap below
// put it on the upper one. It is the only thing that separates a `complete`
// file's mirror from a genuine repeat once both are upper-triangular, and
// those two want opposite treatment — see {@link collapse}.
const swapped = new Uint8Array(rows)
const state: ScanState = { out: 0, line: 0, sawUpper: false, sawLower: false }
let sum = 0
let at = 0
// The tight loop is a **synchronous** function called slice by slice, and the
// yield sits between the calls rather than inside the loop. That shape is not
// stylistic: an `await` inside the scanning loop makes the whole loop part of
// an async function's state machine, and V8 stops optimising it — measured at
// 40 s for a 270 MB file against 2.7 s for the same code with the await moved
// out. The yield is still needed, because a cancel arrives as a message and a
// worker that never returns to its event loop never reads one (`../async`).
//
// The hooks are resolved to real functions *here*, and calling them through
// `?.` in the loop below would undo the paragraph above entirely. V8 inlines
// `scanSlice` back into this function and compiles the loop as one unit; an
// optional call that has never been made carries no type feedback, so that
// unit is thrown away — `Insufficient type feedback for call` — on the first
// slice, recompiled on the next, and thrown away again. The scan then runs
// interpreted, which measured **35 s for a 270 MB file against 0.9 s** here.
// A default that is a function makes both call sites ordinary ones.
const report = hooks.onProgress ?? noReport
const isCancelled = hooks.cancelled ?? notCancelled
while (at < n) {
const stop = lineBoundaryAfter(bytes, Math.min(n, at + SCAN_SLICE))
at = scanSlice(bytes, at, stop, nBins, label, bin1, bin2, count, swapped, state)
await yieldToEventLoop()
if (isCancelled()) throw cancelled()
report(state.out, rows)
}
const out = state.out
const { sawUpper, sawLower } = state
// A file of nothing but its diagonal is in neither triangle and is reported
// as the default one, which is what it would have been written as.
const observed: HicProPixels['observed'] =
sawUpper && sawLower ? 'mixed' : sawLower ? 'lower' : 'upper'
// Two stable counting sorts — by `bin2`, then by `bin1` — which together put
// the pixels in the (row, column) order a cooler stores them in, and leave
// the second pass's bucket boundaries as `bin1_offset` exactly.
//
// A radix sort rather than a sort per row band, and the difference is not
// academic. Sorting each band on its own is quadratic in the band's width,
// and bands are *wide*: a row of a 100 kb human matrix has thousands of
// non-zero columns. Measured on a 211 MB file with wide bands, the per-band
// insertion sort took 59 s where this takes about two — the parse itself runs
// at 100 MB/s and the sort must not be what decides the wait.
const byColumn = countingSort(bin2, out, nBins)
const { order, offsets: binOffset } = countingSortBy(bin1, byColumn, out, nBins)
const sorted1 = new Int32Array(out)
const sorted2 = new Int32Array(out)
const sortedV = new Float32Array(out)
const sortedSide = new Uint8Array(out)
for (let k = 0; k < out; k++) {
const from = order[k]
sorted1[k] = bin1[from]
sorted2[k] = bin2[from]
sortedV[k] = count[from]
sortedSide[k] = swapped[from]
}
const folded = collapse(sorted1, sorted2, sortedV, sortedSide, binOffset, nBins)
for (let k = 0; k < folded.nnz; k++) sum += sortedV[k]
return {
bin1: sorted1.subarray(0, folded.nnz),
bin2: sorted2.subarray(0, folded.nnz),
count: sortedV.subarray(0, folded.nnz),
binOffset: folded.binOffset,
nnz: folded.nnz,
sum,
observed: observed === 'mixed' && folded.mirrored > 0 ? 'complete' : observed,
}
}
/** Text per synchronous slice: big enough that the yield is noise, small
* enough that a cancel is answered within a few tens of milliseconds. */
const SCAN_SLICE = 1 << 23
/** What the slice scanner carries between slices. */
interface ScanState {
out: number
line: number
sawUpper: boolean
sawLower: boolean
}
/** The first byte after the newline at or after `at`, so a slice ends on a row. */
function lineBoundaryAfter(bytes: Uint8Array, at: number): number {
let i = at
while (i < bytes.length && bytes[i] !== NEWLINE) i++
return Math.min(bytes.length, i + 1)
}
/**
* Scan `[from, to)` of a matrix into the arrays, and return where it stopped.
*
* Synchronous, and deliberately a function of its own — see the note at its one
* call site. Everything it touches is a typed array or a number, so the loop
* stays in the shape V8 can keep in registers.
*
* ## Why it reads its own digits rather than calling {@link readInt}
*
* It did call it, and that made this function **nineteen times slower** — but
* only when a bin file had been parsed first, which is to say only ever in the
* application and never in a test that timed the matrix alone. A 270 MB file
* took 35 s where it now takes 1.8 s, and the difference was not in any of the
* arithmetic below.
*
* `--trace-opt-verbose` says what happened: `delaying optimization of
* scanSlice, IC changed`, once per tick, forever. {@link readInt} is shared
* with {@link parseBins}, so its inline caches carry that call's feedback too —
* a different array, different values, different shapes — and V8 will not tier
* up a function whose caches are still moving. The scan therefore ran
* interpreted from the first byte to the last, which is what a 30× gap looks
* like.
*
* So the one hot loop in this reader owns everything it touches. That is not a
* micro-optimisation and it is not a duplicate to be tidied away later: it is
* the only thing separating a two-second open from a thirty-five-second one,
* and reintroducing the call would restore the slow one silently, because every
* test that times this file parses no bins.
*/
function scanSlice(
bytes: Uint8Array,
from: number,
to: number,
nBins: number,
label: string,
bin1: Int32Array,
bin2: Int32Array,
count: Float32Array,
swapped: Uint8Array,
state: ScanState,
): number {
let at = from
let out = state.out
let line = state.line
let sawUpper = state.sawUpper
let sawLower = state.sawLower
while (at < to) {
if (bytes[at] === NEWLINE || bytes[at] === RETURN) {
at++
continue
}
if (bytes[at] === HASH) {
while (at < to && bytes[at] !== NEWLINE) at++
continue
}
line++
// `binA`, then `binB`: unsigned decimal, tab-terminated. A sign here is not
// a bin id, so it ends the number at zero digits and is reported as a row
// that is not `binA binB count` — which it is.
let a = 0
let sawA = false
while (at < to) {
const c = bytes[at]
if (c < ZERO || c > NINE) break
a = a * 10 + (c - ZERO)
sawA = true
at++
}
if (!sawA || bytes[at] !== TAB) throw badMatrix(label, line, nBins)
at++
let b = 0
let sawB = false
while (at < to) {
const c = bytes[at]
if (c < ZERO || c > NINE) break
b = b * 10 + (c - ZERO)
sawB = true
at++
}
if (!sawB || bytes[at] !== TAB) throw badMatrix(label, line, nBins)
at++
// The value column, which is an integer in `raw/` and a float in `iced/`.
let v = 0
let sawV = false
let negative = false
if (bytes[at] === MINUS) {
negative = true
at++
}
while (at < to) {
const c = bytes[at]
if (c < ZERO || c > NINE) break
v = v * 10 + (c - ZERO)
sawV = true
at++
}
if (bytes[at] === DOT) {
at++
let scale = 0.1
while (at < to) {
const c = bytes[at]
if (c < ZERO || c > NINE) break
v += (c - ZERO) * scale
scale /= 10
sawV = true
at++
}
}
// An exponent, which `iced/` writes for very small bias-scaled values.
if (bytes[at] === E_LOWER || bytes[at] === E_UPPER) {
const mark = at
at++
let expSign = 1
if (bytes[at] === MINUS) {
expSign = -1
at++
} else if (bytes[at] === PLUS) {
at++
}
let exp = 0
let sawExp = false
while (at < to) {
const c = bytes[at]
if (c < ZERO || c > NINE) break
exp = exp * 10 + (c - ZERO)
sawExp = true
at++
}
// An `e` with no digits behind it is not an exponent; leave it to the
// skip-to-newline below rather than swallowing the rest of the row.
if (sawExp) v *= 10 ** (exp * expSign)
else at = mark
}
if (!sawV) throw badMatrix(label, line, nBins)
if (negative) v = -v
while (at < to && bytes[at] !== NEWLINE) at++
at++
// 1-based to 0-based. A `0` in either column means the file is already
// 0-based, which HiC-Pro does not write but a hand-made one might; it is
// caught by the bounds check rather than silently shifting every pixel.
const i = a - 1
const j = b - 1
if (i < 0 || j < 0 || i >= nBins || j >= nBins) {
throw new ViewerError(
'format',
`${label} names bin ${a} × ${b} on line ${line}, and the bin file has ` +
`${nBins} bins numbered 1…${nBins}. The two halves of the pair are for different ` +
'resolutions, or for different genomes.',
{ label, line, bin1: a, bin2: b, nBins },
)
}
// Strictly: a diagonal pixel is in neither triangle, and counting it in
// both labelled every real file `mixed` — which every real file has, so the
// label meant nothing until this was strict.
if (i < j) sawUpper = true
if (i > j) sawLower = true
// Stored upper whichever way it arrived; `complete` is folded below.
bin1[out] = i <= j ? i : j
bin2[out] = i <= j ? j : i
count[out] = v
swapped[out] = i <= j ? 0 : 1
out++
}
state.out = out
state.line = line
state.sawUpper = sawUpper
state.sawLower = sawLower
return at
}
/**
* Collapse pixels that landed on the same cell, in place.
*
* One row band at a time, sorting each by column — the bands are short (a row
* of a contact map) so an insertion sort over each beats one comparison sort
* over the whole array, and the CSR order is preserved by construction.
*
* ## Mirrors are dropped; repeats are summed
*
* Two rows can land on one cell, and they mean opposite things:
*
* - a **mirror**, which is what `MATRIX_FORMAT=complete` writes: `(a, b)` and
* `(b, a)` are one contact stated twice, so **adding** them would double
* every off-diagonal cell of the map and leave the diagonal alone — a picture
* that still looks entirely like a contact map;
* - a **repeat**, two rows for the same pair on the same side, which is what a
* file concatenated from two runs holds. Here the second is more evidence,
* and **dropping** it silently loses contacts.
*
* Once both have been swapped onto the upper triangle they are indistinguishable
* — which is why the side each row was *stored* on is carried this far. It is
* the only place the difference is still visible, and it is one byte per pixel
* to keep it.
*/
function collapse(
bin1: Int32Array,
bin2: Int32Array,
count: Float32Array,
side: Uint8Array,
binOffset: Float64Array,
nBins: number,
): { nnz: number; binOffset: Float64Array; mirrored: number } {
let write = 0
let mirrored = 0
const out = new Float64Array(nBins + 1)
for (let row = 0; row < nBins; row++) {
const lo = binOffset[row]
const hi = binOffset[row + 1]
out[row] = write
// The band is already in column order, so equal cells are adjacent and one
// linear pass settles them.
let seenSide = -1
for (let i = lo; i < hi; i++) {
if (i > lo && bin2[i] === bin2[i - 1]) {
if (side[i] !== seenSide) {
// The mirror of one already written: one contact, stated twice.
mirrored++
seenSide = -2
continue
}
// The same pair on the same side again: more of the same contact.
count[write - 1] += count[i]
continue
}
seenSide = side[i]
bin1[write] = row
bin2[write] = bin2[i]
count[write] = count[i]
write++
}
}
out[nBins] = write
return { nnz: write, binOffset: out, mirrored }
}
/**
* A stable counting sort of `0…n` by `key`, returning the new order.
*
* `key` values are bin ids, so they are bounded by the bin count and a counting
* sort is exact and linear — no comparisons, and no allocation beyond the
* buckets and the order itself.
*/
function countingSort(key: Int32Array, n: number, buckets: number): Int32Array {
const counts = new Int32Array(buckets + 1)
for (let i = 0; i < n; i++) counts[key[i] + 1]++
for (let b = 0; b < buckets; b++) counts[b + 1] += counts[b]
const order = new Int32Array(n)
for (let i = 0; i < n; i++) order[counts[key[i]]++] = i
return order
}
/**
* The same sort applied to an existing order, keeping it as the tie-break.
*
* Stability is the whole point: run over an order already sorted by column, it
* produces (row, column) order — and its bucket boundaries, handed back, *are*
* the cumulative `bin1_offset` a cooler stores.
*/
function countingSortBy(
key: Int32Array,
order: Int32Array,
n: number,
buckets: number,
): { order: Int32Array; offsets: Float64Array } {
const offsets = new Float64Array(buckets + 1)
for (let i = 0; i < n; i++) offsets[key[i] + 1]++
for (let b = 0; b < buckets; b++) offsets[b + 1] += offsets[b]
const cursor = Float64Array.from(offsets)
const out = new Int32Array(n)
for (let i = 0; i < n; i++) {
const at = order[i]
out[cursor[key[at]]++] = at
}
return { order: out, offsets }
}
/** The storage mode the rest of the reader is told about — always this one. */
export const HICPRO_STORAGE_MODE: StorageMode = 'symmetric-upper'
// ---------------------------------------------------------------------------
// Scanners
// ---------------------------------------------------------------------------
function readInt(bytes: Uint8Array, at: number): { value: number; at: number; saw: boolean } {
let value = 0
let saw = false
let sign = 1
if (bytes[at] === MINUS) {
sign = -1
at++
}
while (at < bytes.length) {
const c = bytes[at]
if (c < ZERO || c > NINE) break
value = value * 10 + (c - ZERO)
saw = true
at++
}
return { value: value * sign, at, saw }
}
function badMatrix(label: string, line: number, nBins: number): ViewerError {
return new ViewerError(
'format',
`${label} is not a HiC-Pro matrix: line ${line} is not \`binA binB count\`. ` +
`The bin file beside it has ${nBins} bins, and the matrix names pairs of them, ` +
'tab-separated, one pixel per line.',
{ label, line, nBins },
)
}
function cancelled(): Error {
const err = new Error('cancelled')
err.name = 'AbortError'
return err
}
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