Press n or j to go to the next uncovered block, b, p or k for the previous block.
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* The analysis panel, without the panel.
*
* ## Why this exists
*
* The Analysis panel computes sixteen things and every one of them is goldened
* against cooltools, coolpuppy, chromosight, pyBigWig and numpy (§18.10). That is a lot of
* verified arithmetic reachable only by clicking, and the moment a reader has
* two hundred files rather than one, clicking stops being the interface. They
* leave — for cooltools, which is the right tool and a different set of
* definitions, so the numbers in the figure and the numbers in the table are no
* longer the same numbers.
*
* So: the same kernels, the same writers, the same provenance lines, driven from
* a shell. Not a reimplementation and not a port — `RUNNERS` and `TRACK_RUNNERS`
* are imported from `analysis/run/`, and the job handed to each is built exactly
* as `analysis/worker/analysis.worker.ts` and
* `annotations/worker/annotations.worker.ts` build theirs. If the two ever
* disagree, one of them is wrong and there is a golden that says which.
*
* **Both maps, because there are two venues.** A task states which worker it
* belongs in (`analysis/job.ts`), and reading only `RUNNERS` is what made this
* command list sixteen tasks and honour twelve: `motif`, `metaplot`, `trackcorr`
* and `overlap` were offered with a flag per parameter and then died with *no
* analysis runner is registered* — after the mount, once per file, exit 1.
*
* **Every task, because the console records every run.** For a while the
* shell honoured what it could and refused the rest by name: the three tasks
* that read a bigWig, the one that reads a second map, and any run made in a
* session with no contact map. Each refusal was honest and each was a hole in
* the console (§23) exactly where a reader looks for a line to paste — a
* metaplot over two hundred files is the run somebody most wants as a command.
* So the four capabilities a shell was said not to have are now here, each as
* the same code the worker runs:
*
* - **Tracks.** `--tracks` opens a bigWig, a bedGraph, a wig or a FASTA where it
* lies (`cli/tracks.ts`), and `sample` answers from it in the annotations
* worker's own shape. A FASTA named for `compartments`' phasing becomes the
* per-bin GC vector the session would have shipped.
* - **A second map.** `--against` names the files `hicrep` compares this one
* with, and `peer` mounts each one exactly as the analysis worker does.
* - **No map at all.** A task of the annotations venue runs with no file
* positional, over the assembly the tracks declare — the 1D browser's own
* framing (§5.8), so a run made there is a run this can repeat.
* - **A named `.pairs`.** `pairsqc --pairs` (and the retired `expected
* --stranded --pairsUri`) reads a local path through `openFile`, and a
* `.pairs` given as the map carries what its import counted into the run —
* the four orientation curves and `pairtools stats` — as an import in the
* app does, and its own file for a task that reads the records again.
*
* A composite (`magnetwork` requires `magqc`) runs its requirements first, at
* their defaults — or as the task's own flags answered them for it, Pairs QC's
* reference and enzyme being the restriction step's — exactly as
* `AnalysisRunner.plan` does.
*
* ## And why `replay` is the half that matters
*
* A subcommand per task is useful and obvious. The subcommand that is neither is
* `replay`: it takes a **workspace file** — the thing the save button already
* produces, every open tab in one file — and re-runs the analyses recorded in
* one of its tabs over any number of other files. That closes the loop the app is missing at both ends. A
* reader chooses parameters the way parameters should be chosen, by looking at a
* picture and adjusting until it is right; and then applies exactly those, with
* no retyping and no transcription error, to the other hundred and ninety-nine.
*
* ## The two things it does differently, and why
*
* **A remote file is fetched first, whole.** `RemoteRangeSource` reads through
* synchronous `XMLHttpRequest`, which exists in a worker and not in Node, so an
* address cannot be read by range from here. It is downloaded to a temporary
* directory instead and read where it lies (`cli/remote.ts`) — which is what the
* README always said happened, and for a while did not: the address went to
* `stat` as a path.
*
* **No dependencies beyond the app's own.** Argument parsing, colouring and
* table formatting are here rather than depended on, which is the same rule
* `package.json` already applies to the bundle. The parser is typed by the
* task descriptors (`parseArgs`), which is the one thing no general-purpose
* parser could have done for it: whether `--stranded` takes the word after it
* is a fact about the task.
*/
import { existsSync, readFileSync, realpathSync } from 'node:fs'
import { readFile, mkdir, writeFile } from 'node:fs/promises'
import { deflateSync } from 'node:zlib'
import { basename, dirname, join, resolve } from 'node:path'
import { fileURLToPath, pathToFileURL } from 'node:url'
import { isMainThread } from 'node:worker_threads'
import { MetaCooler } from '../metacooler/MetaCooler'
import { LocalFileSource } from '../sources/LocalFileSource'
import { inflationCap } from '../sources/untrusted'
import { yieldToEventLoop } from '../async'
import { chosenEntries } from '../analysis/runner'
import { RUNNERS } from '../analysis/run/index'
import { TRACK_RUNNERS } from '../analysis/run/tracks'
import { TASKS, taskById } from '../analysis/registry'
import { ENTRY_KINDS, OUTPUT_FILES, taskCatalogue } from '../analysis/catalogue'
import { abortError, runnerParams } from '../analysis/job'
import type { JobContext, SequenceReader, TrackJobContext } from '../analysis/job'
import {
gcTrack,
lengthsOf,
loadTracks,
samplerOver,
trackFor,
vectorOver,
type LoadedTrack,
} from './tracks'
import { outputToTsv } from '../analysis/write/tsv'
import { gridAt } from '../analysis/context'
import {
CIRCULAR_SCORE,
JUNCTION_BINS,
MIN_JUNCTION_SEQUENCE_BINS,
junctionCandidates,
junctionQuorum,
measureJunctions,
placeCandidate,
} from '../analysis/circularity'
import { profileToBedGraph, type BedGraphContig } from '../analysis/write/bedgraph'
import { writeBigWig } from '../analysis/write/bigwig'
import {
WHOLE_FILE_INFLATION,
decodeAnnotationBytes,
decodeAnnotationText,
parseBed,
parseBedpe,
parseGtf,
sniffFormat,
} from '../annotations/parse'
import { parseBarChart, sniffBarChart } from '../annotations/barchart'
import { parseCytoBand, sniffCytoBand } from '../annotations/cytoband'
import { parseGenePred, sniffGenePred } from '../annotations/genepred'
import { parseInteract, sniffInteract } from '../annotations/interact'
import { parseJunctions, sniffJunctions } from '../annotations/junctions'
import { parseLongRange, sniffLongRange } from '../annotations/longrange'
import { parseVcf, sniffVcf } from '../annotations/vcf'
import { formatIntervals } from '../annotations/export'
import { cleanLabel } from '../annotations/names'
import { parseBed3d, parseG3d, sniffBed3d, sniffG3d, writeBed3d } from '../annotations/g3d'
import { parsePdb, pdbRefusal, sniffPdb, writePdb } from '../annotations/pdb'
import type { FeatureSet, PairSet, StoredEntry } from '../annotations/types'
import { hicProBinsNames, isHicProMatrix } from '../annotations/sidecar'
import { openReference, type Reference } from './reference'
import { Downloads, SIDE_CACHE_BYTES, addressDirectories, displayOf, fileNameOf, isAddress } from './remote'
import { DEFAULT_THREADS, serveIfHelper, useThreads } from './threads'
import { quote, referenceKeyOf } from '../analysis/cliCommand'
import { regionLabel, typedLocusToRegion } from '../genome/assembly'
import { parseBins } from '../hicpro/parse'
import { DEFAULT_COUNT_COLUMN } from '../metacooler/matrix'
import { BOOST_ALPHA, BOOST_MAX_BINS, boostSteps } from '../metacooler/boost'
import { cisSquare } from '../metacooler/resample'
import { contactsText, depthPhrase, parseContacts, type DrawnDepth } from '../contacts'
import { hicProMap } from '../worker/open'
import { isRefusal, refusalMessage } from '../state/SessionConfig'
import { parseWorkspaceFile } from '../state/workspace'
import {
defaultParams,
paramDerived,
type AnalysisFraming,
type AnalysisTask,
type ParamSpec,
type ParamValue,
type Params,
type TaskOutput,
type TaskResult,
upstreamParamsOf,
} from '../analysis/types'
import type { PeerMap, TaskInputs } from '../analysis/worker/protocol'
import type { OrientationSummary, SourceSpec } from '../worker/protocol'
import { importPairs, probePairs } from '../pairs/import'
import { binPairs } from '../pairs/bin'
import { isPairsFile, readPairsHeader } from '../pairs/format'
import { writePairtoolsStats, type PairStats } from '../pairs/stats'
import { ViewerError } from '../errors'
import { parseUri } from '../uri'
import type { ByteSource } from '../types'
import { COMMIT, VERSION } from '../version'
import { DOCS_URL } from '../documentation/site'
/**
* Which build wrote a file, after the `# chromosomix` every export opens with:
* the version and `cli`, as the app's own exports give its version and commit.
* The command shares the app's name, so naming it here as well would print it
* twice.
*/
const APP = `${VERSION} cli`
// ---------------------------------------------------------------------------
// Arguments
// ---------------------------------------------------------------------------
export interface Args {
command: string
positional: string[]
flags: Map<string, string[]>
}
/**
* A fault in the command line itself — a flag nothing takes, a value that is
* not one, a switch handed a word.
*
* Exit 2 with the sentence, before any file is opened, against 1 for a file
* that failed: a command that is wrong should say so before it spends an hour
* being wrong two hundred times.
*/
class UsageError extends Error {}
/** One flag a command takes, as the parser needs it. */
interface FlagSpec {
/** A switch takes nothing after it; a value flag takes the word after it. */
arity: 'switch' | 'value'
/** Where it is filed: `--no-stranded` files `false` under `stranded`. */
key: string
/** `--no-x`, the switch that turns `x` off. */
negates: boolean
}
/**
* The words a switch's value may be written as, and what each means.
*
* Only after `=`: `--stranded=false`. The same words written *after* a switch,
* as a word of their own, are refused (`parseArgs`), since that was how a
* switch was turned off when switches took the word after them.
*/
const SWITCH_WORDS: ReadonlyMap<string, boolean> = new Map([
['true', true],
['false', false],
['yes', true],
['no', false],
['on', true],
['off', false],
['1', true],
['0', false],
])
/** Whether a parameter is on or off — the rule `coerce` reads it by. */
function isSwitch(param: ParamSpec): boolean {
return param.kind === 'toggle' || typeof (param as { default?: unknown }).default === 'boolean'
}
/**
* Every flag `command` takes, and what each takes after it.
*
* The CLI's own first, and then the task's, from its descriptor — which is what
* makes the parse typed: a toggle is a switch, `--no-` before its key turns it
* off, and anything else takes a value. The task's are entered last, so a name
* both use — coverage's `--balance`, apa's `--window` — has the task's meaning,
* which is `paramsFor`'s rule as well. `--no-balance` stays the CLI's: it reads
* the raw counts, framing and parameter alike, and is never the negation of
* coverage's own `--balance`.
*/
function flagsFor(command: string): Map<string, FlagSpec> {
const table = new Map<string, FlagSpec>()
for (const key of RESERVED) {
table.set(key, { arity: SWITCHES.has(key) ? 'switch' : 'value', key, negates: false })
}
// A switch wherever it is written, so that `main` refuses it by name — it is
// the default now — rather than the file after it being taken as its value.
table.set('balance', { arity: 'switch', key: 'balance', negates: false })
if (command === 'replay') table.set('tab', { arity: 'value', key: 'tab', negates: false })
// `boost` is no task either, so its own two are named here, as `replay`'s `--tab` is.
if (command === 'boost') {
for (const key of ['sequences', 'alpha']) table.set(key, { arity: 'value', key, negates: false })
}
for (const param of taskById(command)?.params ?? []) {
const on = isSwitch(param)
table.set(param.key, { arity: on ? 'switch' : 'value', key: param.key, negates: false })
const off = `no-${param.key}`
if (on && !RESERVED.has(off)) table.set(off, { arity: 'switch', key: param.key, negates: true })
}
return table
}
/** The sentence for a flag `command` does not take. */
function unknownFlag(command: string, name: string): string {
const task = taskById(command)
if (task !== undefined) {
return (
`${task.id} has no parameter --${name}. Its parameters are: ` +
`${task.params.map((entry) => `--${entry.key}`).join(', ') || '(none)'}.`
)
}
return `${command} has no flag --${name}. \`chromosomix help\` lists the ones it takes.`
}
/**
* The command: the first word that is neither a flag nor the value of one.
*
* Only the CLI's own flags may come before it, because only theirs are known
* before the command is — what a task's `--x` takes is a fact about the task.
* A task's flag ahead of its task is refused rather than guessed at, unless the
* line holds no command at all (`chromosomix --verbose`), which is the usage.
*/
function commandOf(argv: readonly string[]): string {
const own = flagsFor('')
for (let at = 0; at < argv.length; at++) {
const token = argv[at]
if (!token.startsWith('--')) return token
const body = token.slice(2)
if (body.includes('=')) continue
const spec = own.get(body)
if (spec === undefined) {
if (argv.slice(at + 1).every((rest) => rest.startsWith('--'))) return ''
throw new UsageError(
`--${body} is not one of the command line's own flags, and a task's flags come after the ` +
`task: chromosomix <task> <file> --${body} …`,
)
}
if (spec.arity === 'value') at += 1
}
return ''
}
/**
* `--key value`, `--key=value`, `--switch`, `--no-switch`, and every other word
* positional — typed by what `command` takes.
*
* It was untyped: a flag took the next word as its value unless that word began
* with `--`. So `coverage a.cool --no-balance b.hic --out d` read `b.hic` as the
* value of `--no-balance`, ran over `a.cool` alone and exited 0;
* `coverage --quiet a.cool` read the file as `--quiet`'s value and refused
* itself for having none; and `--out --quiet` wrote into a directory called
* `true`. Now a switch never takes the word after it, a flag that takes a value
* is refused without one, and a flag nothing takes is refused by name — for
* `replay` and `circular` as for a task, since a typo in a batch that runs for
* an hour must not quietly run the default.
*
* A switch's old value written as a word, `--stranded false`, is refused rather
* than read as a file called `false`: the script that wrote it meant something
* else by it, and is told what to write instead.
*
* Repeated keys accumulate, because `--features a.bed --features b.bed` is a
* question a reader will ask and silently keeping the last one is the wrong
* answer to it.
*/
function parseArgs(argv: readonly string[], command: string): Args {
const table = flagsFor(command)
const positional: string[] = []
const flags = new Map<string, string[]>()
const push = (key: string, value: string): void => {
const held = flags.get(key)
if (held === undefined) flags.set(key, [value])
else held.push(value)
}
for (let at = 0; at < argv.length; at++) {
const token = argv[at]
if (!token.startsWith('--')) {
positional.push(token)
continue
}
const body = token.slice(2)
const eq = body.indexOf('=')
const name = eq >= 0 ? body.slice(0, eq) : body
const spec = table.get(name)
if (spec === undefined) throw new UsageError(unknownFlag(command, name))
if (spec.arity === 'value') {
if (eq >= 0) {
push(spec.key, body.slice(eq + 1))
continue
}
const next = argv[at + 1]
if (next === undefined || next.startsWith('--')) {
throw new UsageError(`--${name} needs a value after it: --${name} <value>.`)
}
push(spec.key, next)
at += 1
continue
}
if (eq >= 0) {
if (spec.negates) {
throw new UsageError(`--${name} takes no value: it is --${spec.key}=false already.`)
}
push(spec.key, String(switchValue(name, body.slice(eq + 1))))
continue
}
const next = argv[at + 1]
const meant = next === undefined ? undefined : SWITCH_WORDS.get(next.toLowerCase())
if (meant !== undefined) {
throw new UsageError(
`--${name} is a switch and takes nothing after it, so “${next}” would be read as a file. ` +
`Write ${switchAdvice(table, name, spec, meant)} — or ./${next}, if it is a file.`,
)
}
push(spec.key, spec.negates ? 'false' : 'true')
}
// The command is the first positional by construction: before it, only the
// CLI's own flags can stand, and they take here what `commandOf` took.
return { command: positional[0] ?? '', positional: positional.slice(1), flags }
}
/**
* A line as `main` reads it — its command, its files and its flags — or the
* refusal `main` would print, thrown. Exported so that the lines the console
* writes (`analysis/cliCommand.ts`) can be held to the parser that has to take
* them, which is the one place the two meet.
*/
export function parseCommandLine(argv: readonly string[]): Args {
return parseArgs(argv, commandOf(argv))
}
/**
* What to write for `--name <word>`, where the word meant `meant`: the switch
* alone to say yes, and its `=false` — or its `--no-` — to say no.
*/
function switchAdvice(
table: ReadonlyMap<string, FlagSpec>,
name: string,
spec: FlagSpec,
meant: boolean,
): string {
// `--no-stranded false` is a double negative, and the switch it negates is
// the plain way to say what it means.
if (spec.negates) return meant ? `--${name} alone` : `--${spec.key}`
if (meant) return `--${name} alone`
return table.get(`no-${spec.key}`)?.negates === true
? `--${name}=false or --no-${spec.key}`
: `--${name}=false`
}
/** An explicit switch value, `--stranded=off`, as the boolean it means. */
function switchValue(name: string, text: string): boolean {
const value = SWITCH_WORDS.get(text.trim().toLowerCase())
if (value === undefined) {
throw new UsageError(
`--${name}=${text}: a switch is true or false, or yes or no, on or off, 1 or 0.`,
)
}
return value
}
const one = (args: Args, key: string): string | undefined => args.flags.get(key)?.[0]
const all = (args: Args, key: string): string[] => args.flags.get(key) ?? []
/**
* `--bin-size` and `--rungs`, or `undefined` when neither was given.
*
* Only consulted for a `.pairs`, and harmless everywhere else: a cooler states
* its own resolutions, so a bin size named on the command line for one would be
* a second answer to a question the file already answered.
*
* Read once, before any file is opened, and refused when it is not a whole
* number: `--rungs abc` built one rung and said nothing, and `--bin-size 0` was
* taken for no bin size at all. `--binsize` is the task's where the task claims
* the name — track correlation's window — as `--window` is apa's.
*/
function pairsBinningOf(args: Args, task?: AnalysisTask): PairsBinning | undefined {
const claimed = task?.params.some((param) => param.key === 'binsize') === true
const named = one(args, 'bin-size') ?? (claimed ? undefined : one(args, 'binsize'))
if (named === undefined) return undefined
const base = numberValue('bin-size', named)
if (!Number.isInteger(base) || base < 1) {
throw new UsageError(`--bin-size is a whole number of base pairs, 1 or more; got “${named}”.`)
}
const asked = one(args, 'rungs')
const rungs = asked === undefined ? 1 : numberValue('rungs', asked)
if (!Number.isInteger(rungs) || rungs < 1) {
throw new UsageError(`--rungs is how many resolutions to build, 1 or more; got “${asked}”.`)
}
return { base, rungs }
}
/**
* `--value`, `--circular` and `--cell`: the framing a session sets from the
* picture, spelled as flags (see `RESERVED`).
*/
function framingFlags(
args: Args,
task?: AnalysisTask,
): Pick<RunOptions, 'value' | 'circular' | 'cells' | 'origins' | 'contacts' | 'coarsen'> {
const value = one(args, 'value')
const contacts = contactsOf(args, task)
const coarsen = coarsenOf(args)
return {
...(value === undefined || value === '' ? {} : { value }),
...(contacts === undefined ? {} : { contacts }),
...(coarsen === undefined ? {} : { coarsen }),
circular: all(args, 'circular').flatMap((item) => item.split(',')).filter((item) => item !== ''),
cells: all(args, 'cell').flatMap((item) => item.split(',')).filter((item) => item !== ''),
origins: originsOf(all(args, 'origin')),
}
}
/**
* `--coarsen BP`: the resolution to read the map at (§3.4), a whole number of
* the file's bins summed — what the app writes for a run on a resolution the
* reader added. Digits may be grouped, as the app prints them.
*/
function coarsenOf(args: Args): number | undefined {
const text = one(args, 'coarsen')
if (text === undefined) return undefined
const binsize = numberValue('coarsen', text.replace(/[,_]/g, ''))
if (!Number.isInteger(binsize) || binsize < 1) {
throw new UsageError(`--coarsen is a bin size in whole base pairs; got “${text}”.`)
}
return binsize
}
/**
* A map read at `binsize` (§3.4): its own bins summed, a whole number at a
* time, as the app reads a resolution the reader added — or the map itself,
* where its bins are that size already.
*/
function atResolution(mc: MetaCooler, binsize: number, path: string): MetaCooler {
if (binsize === mc.binsize) return mc
const factor = binsize / mc.binsize
if (!Number.isInteger(factor) || factor < 1) {
throw new Error(
`--coarsen ${binsize}: ${fileNameOf(path)} is at ${mc.binsize.toLocaleString('en-US')} bp, and ` +
`${binsize.toLocaleString('en-US')} bp is not a whole number of its bins: name a bin size ` +
'that is, or open the file at a resolution that divides this one.',
)
}
const seen = MetaCooler.coarsened(mc, factor)
if (seen.refusal !== null) throw new Error(`--coarsen ${binsize}: ${seen.refusal}`)
return seen.map
}
/**
* `--contacts N`: the total to draw the map to (§6.5), typed as the breadcrumb's
* box takes it — `10M`, `23,000,000`, `2.5e7`.
*/
function contactsOf(args: Args, task?: AnalysisTask): number | undefined {
// Only the words the task does not claim: Compartments' `--contacts cis` is
// its own choice, and the total beside it on the same line is this (`shareOf`).
const text = shareOf(task, 'contacts', all(args, 'contacts')).own[0]
if (text === undefined) return undefined
const parsed = parseContacts(text)
if (parsed === null) return undefined
if (typeof parsed !== 'number') {
const param = task?.params.find((entry) => entry.key === 'contacts')
if (param?.kind === 'choice') {
const choices = param.options.map((option) => option.value).join(', ')
throw new UsageError(
`--contacts ${text} is neither a choice of ${task?.id} (${choices}) nor a number of ` +
'contacts to draw the map to: type one like 10M or 23,000,000.',
)
}
throw new UsageError(`--contacts: ${parsed.refused}`)
}
return parsed
}
/**
* `--origin NAME:POS`, repeated or comma-separated: where each sequence's
* replication origin is (§8.15), in the **display** form — 1-based, the number
* the Origin and terminus table prints — and kept 0-based in the framing, like
* every coordinate a worker is handed (§26.1). Digit grouping is allowed, since
* the number is copied from a table that groups it.
*/
function originsOf(items: readonly string[]): Record<string, number> {
const out: Record<string, number> = {}
// A comma separates two origins only where a name and its colon follow it:
// `LR657304.1:6,374,501` — the form the framing line prints — is one origin
// with its digits grouped, not three.
for (const item of items.flatMap((entry) => entry.split(/,(?=[^,]*:)/))) {
const at = item.lastIndexOf(':')
if (at <= 0) {
if (item.trim() !== '') throw new Error(`--origin ${item} is not NAME:POSITION.`)
continue
}
const name = item.slice(0, at)
const position = Number(item.slice(at + 1).replace(/[,_]/g, ''))
if (!Number.isFinite(position) || position < 1) {
throw new Error(`--origin ${item}: the position is 1-based and at least 1.`)
}
out[name] = Math.floor(position) - 1
}
return out
}
/** `LR657304.1:6,374,501` — the origins as a reader would type them back. */
function originLabel(origins: Readonly<Record<string, number>>): string {
return Object.entries(origins)
.map(([name, at]) => `${name}:${(at + 1).toLocaleString('en-US')}`)
.join(', ')
}
const flag = (args: Args, key: string): boolean => {
const value = one(args, key)
return value !== undefined && value !== 'false'
}
// ---------------------------------------------------------------------------
// Parameters
// ---------------------------------------------------------------------------
/**
* Turn `--window 100000` into the typed value the descriptor expects.
*
* Driven by the descriptor rather than by guessing, so a numeric parameter
* cannot arrive as the string `"100000"` and a boolean cannot arrive as
* `"false"` — both of which a runner would read as truthy and act on. An unknown
* key is an error rather than being ignored: a typo in a batch script that runs
* for an hour must not silently use the default. And so is a value the form
* could not have held ({@link refusalOf}), for the same reason.
*/
/**
* The words of a flag the command line and the task both use, shared out by what
* each can mean (§23.1).
*
* The rule elsewhere is one name, one meaning, decided by whether the task
* claims it: apa's `--window` is its half-width and never the locus, coverage's
* `--balance` its own switch. `--contacts` is the exception that rule cannot
* serve. It is the total a map is drawn to (§6.5) on every task, and it is also
* Compartments' own choice of which contacts to correlate — and the console
* writes both on one line, `--contacts cis --contacts 10000000`. Given wholly to
* the task, the total of a drawn map was lost from every compartments line;
* given wholly to the command line, `cis` was read as a total and refused, which
* is what every compartments line the console had ever written did.
*
* The two meanings never meet: a choice is one of a handful of words and a total
* is a number. So where the task's parameter of that name is a choice, its
* options are the task's and every other word is the command line's; where it is
* anything else, the task has the name outright, as it always had.
*/
function shareOf(
task: AnalysisTask | undefined,
key: string,
values: readonly string[],
): { task: string[]; own: string[] } {
const param = task?.params.find((entry) => entry.key === key)
if (param === undefined) return { task: [], own: [...values] }
if (param.kind !== 'choice') return { task: [...values], own: [] }
const options = new Set(param.options.map((option) => option.value))
return {
task: values.filter((value) => options.has(value)),
own: values.filter((value) => !options.has(value)),
}
}
function paramsFor(task: AnalysisTask, args: Args): Params {
// Built as a mutable record and returned as `Params`, which is readonly: the
// type is a promise to the *runners* that nothing edits their parameters mid
// run, not a claim that nobody may assemble one.
const params: Record<string, Params[string]> = {}
const known = new Map(task.params.map((param) => [param.key, param]))
for (const param of task.params) {
// A number whose default is the context's (`NumberParam.seed`) is left
// unanswered, and the runner decides it from the framing — the map's own
// resolution where a map was named — as the form would have.
if (param.kind === 'number' && param.seed !== undefined) continue
// Nor a parameter the form answers from the file (`paramDerived`) — *use
// balancing weights* — which `runOne` answers from the file it opens.
if (paramDerived(param)) continue
if ('default' in param && param.default !== undefined) {
params[param.key] = param.default as Params[string]
}
}
for (const [key, values] of args.flags) {
const param = known.get(key)
// The task's own parameters win over the CLI's flags where the names
// collide: coverage's own `--balance`, which is off by default, is that
// task's and not the framing's. Skipping a reserved name first would have
// set the framing and left the task at its default, which is precisely the
// silent-default failure the unknown-key error below exists to prevent.
if (param === undefined && RESERVED.has(key)) continue
// `parseArgs` has refused it already, against the same table; said again
// here because this is the function whose silence would cost the hour.
if (param === undefined) throw new UsageError(unknownFlag(task.id, key))
// Of a flag the command line shares, only the task's own words (`shareOf`).
const share = RESERVED.has(key) ? shareOf(task, key, values).task : values
if (share.length === 0) continue
params[key] = coerce(param, share)
}
// `--no-balance` answers the parameter the file otherwise would: off, as the
// framing then is.
if (flag(args, 'no-balance')) {
for (const param of task.params) if (paramDerived(param)) params[param.key] = false
}
for (const param of task.params) {
const refused = refusalOf(param, params[param.key])
if (refused !== null) throw new UsageError(refused)
}
return params
}
/**
* Why `value` cannot be handed to a runner as `spec`, or `null` when it can.
*
* The runners read a choice with a fallback — `strParam(params, 'quantity',
* 'density') === 'expected'` — so that a stored session from a later build
* cannot change what the numbers on screen mean. The form never reaches it: it
* moves a held value onto an option it offers before any run
* (`resolveChoiceDefaults`). A shell had no such step, so `expected --quantity
* expectd` ran the density and wrote `# param quantity: expectd` above it — a
* provenance naming a computation nobody performed — and a replayed workspace
* naming an option this build has not got did the same. So the shell asks what
* the form would have offered, and refuses the rest with the values there are.
* A switch and a number the same way, since `boolParam` and `numParam` fall back
* too, for anything that is not one.
*
* Every option the descriptor lists, not only those this file is offered:
* which those are is a fact about a file that is not open yet, and the runner
* refuses the rest by name — a per-genome P(s) of a cooler is a sentence, not a
* fallback.
*/
function refusalOf(spec: ParamSpec, value: ParamValue | undefined): string | null {
if (value === undefined) return null
// The text `"false"` is not `false`, and a sentence saying so has to show
// which of the two it was handed.
const shown = typeof value === 'string' ? `the text “${value}”` : JSON.stringify(value)
switch (spec.kind) {
case 'choice': {
const values = spec.options.map((option) => option.value)
if (typeof value === 'string' && values.includes(value)) return null
const named = typeof value === 'string' ? `“${value}”` : shown
return `There is no --${spec.key} ${named}. It is ${eitherOf(values.map(quote))}.`
}
case 'toggle':
return typeof value === 'boolean' ? null : `--${spec.key} is true or false, not ${shown}.`
case 'number':
case 'seed':
// `null` is a number the context decides (`NumberParam.seed`), as a
// workspace records one the reader never typed.
return value === null || (typeof value === 'number' && Number.isFinite(value))
? null
: `--${spec.key} is a number, not ${shown}.`
default:
return null
}
}
/** `a`, `a or b`, `a, b or c`. */
function eitherOf(values: readonly string[]): string {
if (values.length <= 1) return values[0] ?? ''
return `${values.slice(0, -1).join(', ')} or ${values[values.length - 1]}`
}
/**
* A number as a reader types one: digits, a point, an exponent.
*
* Not `Number` alone, which reads `''` as zero — so `--factor=` ran at a factor
* of nought and recorded it — and `0x10` as sixteen.
*/
const NUMBER = /^[+-]?(\d+(\.\d*)?|\.\d+)(e[+-]?\d+)?$/i
function numberValue(key: string, text: string): number {
const parsed = NUMBER.test(text.trim()) ? Number(text.trim()) : Number.NaN
if (!Number.isFinite(parsed)) {
throw new UsageError(`--${key} needs a number; got ${JSON.stringify(text)}.`)
}
return parsed
}
/**
* A task's parameters with the ones the file answers filled in.
*
* *Use balancing weights* is the one there is (`BALANCE_PARAM`). A form never
* shows it and sets it from the file (`ParamForm`), and a shell now does the
* same: on wherever the file carries weights, as the framing is — so a command
* that says nothing about balancing reads what the app would have read. Only
* where the command left it open: `--no-balance` has already answered it.
*/
function withDerived(task: AnalysisTask, params: Params, balance: boolean): Params {
if (!task.params.some((spec) => paramDerived(spec) && params[spec.key] === undefined)) return params
const out: Record<string, Params[string]> = { ...params }
for (const spec of task.params) {
if (paramDerived(spec) && out[spec.key] === undefined) out[spec.key] = balance
}
return out
}
/**
* Whether `--balance` means something to this command.
*
* Balanced counts are the default wherever the file carries weights, so the
* flag that used to ask for them asks for nothing — and a flag that asks for the
* default reads as though the default were the other one, which is how a run
* came out unbalanced three times over for want of it. It survives only as a
* task's own parameter where one is declared and is *not* the file's to answer:
* coverage's, which is off because raw coverage is the point of it.
*/
function takesBalance(command: string): boolean {
return (
taskById(command)?.params.some((spec) => spec.key === 'balance' && !paramDerived(spec)) ?? false
)
}
/**
* Flags that belong to the CLI rather than to a task.
*
* Consulted only for a name the task does *not* declare. `--no-balance` reads
* the raw counts: it sets the framing, and the `balance` parameter of every task
* whose form answers it from the file, because a reader typing it once means
* both (`paramsFor`, `withDerived`).
*
* `--window` rather than `--region`: the reconstruction and the model
* comparison both take a parameter called `region`, meaning *which sequences*,
* and the framing's window is a different question. One name for two things is
* how a batch script comes out subtly wrong.
*/
const RESERVED = new Set([
'out',
'o',
'window',
'no-balance',
'features',
'pairs',
'sequence',
// A track to load without a parameter choosing it, for `replay`: a workspace
// records the app's entry ids under `tracks`, and this is how the file behind
// one is named. A direct run needs no such flag — the task's own `--tracks`
// is a path, and loads what it names.
'track',
// The other maps `hicrep` compares this one with (§16). A shell has one file
// and one mount, and this is the flag that stands in for the deck.
'against',
// The three facts of a *framing* a session sets from the picture and a shell
// has to be told: which score column the map is drawn from (§3.5), which
// sequences the reader declared circular (§8.15), and which cells of an
// `.scool` are ticked (§3.8). Each is an input to the arithmetic, so a line
// without them repeats a different run.
'value',
'circular',
// Where each sequence's replication origin is (§8.15), which the arm-frame
// expectation and the inter-arm alignment read their arms from.
'origin',
'cell',
'over',
// How many threads the tasks that share their work may use (`cli/threads.ts`).
// A property of the machine, not of the run: the results are the same bits on
// any number, so a line without it repeats the same run.
'threads',
'quiet',
'help',
'version',
// How a `.pairs` positional is binned (§3.7). Reserved rather than declared
// per task because it is a property of the *input*, not of the analysis: it
// decides which grid the file is read on, and every task then runs on that
// grid exactly as it would over a cooler.
'bin-size',
'binsize',
'rungs',
// The total the map is drawn to before any task reads it (§6.5): a subsample
// below the file's own, an oversample through Boost-HiC above it. A property
// of the input, like the binning, so every task reads the drawn map.
'contacts',
// The resolution it is read at, where that is the file's bins summed (§3.4):
// a property of the input too, for the same reason.
'coarsen',
])
/**
* Of those, the ones that take no value: `--quiet`, and never `--quiet true`.
*
* What `parseArgs` is typed by, with each task's toggles. The rest take the
* word after them, and refuse to be the last word on the line.
*/
const SWITCHES = new Set(['no-balance', 'quiet', 'help', 'version'])
function coerce(param: AnalysisTask['params'][number], values: string[]): Params[string] {
const kind = (param as { kind?: string }).kind
// `sequences` by name as well as `multi`, and it is not a tidy-up: the runners
// read that key with `Array.isArray` and fall back to *every sequence* when it
// is anything else. A plain string is anything else, so `--sequences chr18`
// typed at a shell scanned all twenty-one of them and reported a number from
// the wrong one — a silent widening, which is the failure mode a batch script
// cannot see. It has no `default`, so the array rule below never caught it.
const multiple = (param as { multiple?: boolean }).multiple === true
if (
kind === 'multi' ||
kind === 'sequences' ||
multiple ||
Array.isArray((param as { default?: unknown }).default)
) {
// A list may arrive as repeated flags or as one comma-separated value; both
// are things a shell user will write and neither is wrong.
return values.flatMap((value) => value.split(',')).filter((value) => value !== '')
}
const value = values[values.length - 1]
// A switch's value is `true` or `false` by the time it is here — `parseArgs`
// files `--no-x` and `--x=off` that way — and anything else is refused, where
// every word but `false` and `0` used to be read as on: `--x=no` was a yes.
if (isSwitch(param)) return switchValue(param.key, value)
if (kind === 'number' || typeof (param as { default?: unknown }).default === 'number') {
return numberValue(param.key, value)
}
return value
}
// ---------------------------------------------------------------------------
// Running one task on one file
// ---------------------------------------------------------------------------
interface RunOptions {
task: AnalysisTask
params: Params
path: string
/**
* The command's addresses: how a map named by one is read — by range, or
* from a copy fetched whole — and what a run names as it goes, an
* `--against` or a `.pairs`. A map is opened *as* the address the reader
* typed, so its framing, its provenance and every sentence about it name
* that rather than a temporary file.
*/
downloads: Downloads
window?: string | undefined
balance?: boolean | undefined
inputs: TaskInputs
/**
* References named with `--sequence`, by the string the reader typed.
*
* Beside `inputs` rather than inside it, because {@link TaskInputs} is what
* crosses a `postMessage` and a parsed genome is the one input this codebase
* deliberately never sends anywhere (`analysis/job.ts`, {@link SequenceReader}).
* Here it does not have to: the store and the runner are on one stack.
*/
sequences: Map<string, Reference>
/**
* Tracks named with `--tracks` or `--track`, by the string the reader typed.
*
* Beside `inputs` for the reason `sequences` is: a bigWig handle is the one
* thing the annotations worker exists to hold and never ship, and here it
* need not be shipped — `sample` is answered on the same stack.
*/
tracks: Map<string, LoadedTrack>
/** The other maps a task that compares files is run against (`--against`). */
peers: readonly string[]
/** The score column to read, or `undefined` for the count (§3.5). */
value?: string | undefined
/** Sequences declared circular (§8.15), by this file's names. */
circular: readonly string[]
/** Declared replication origins, 0-based base pairs by this file's names (§8.15). */
origins: Readonly<Record<string, number>>
/** The cells of an `.scool` to sum; empty is every cell (§3.8). */
cells: readonly string[]
quiet: boolean
/** How to bin a `.pairs`, which states no resolution of its own (§3.7). */
binning?: PairsBinning | undefined
/** The total the map is drawn to before the task reads it (§6.5). */
contacts?: number | undefined
/** The bin size the map is read at, its own bins summed (§3.4). */
coarsen?: number | undefined
}
/**
* Draw an open map to `contacts` (§6.5), saying on stderr what the census counted
* and which way it went; `null` when no total was asked for.
*/
async function drawnTo(
mc: MetaCooler,
contacts: number | undefined,
quiet: boolean,
): Promise<DrawnDepth | null> {
if (contacts === undefined) return null
const plan = await mc.resample({ contacts })
if (plan === null) return null
const depth: DrawnDepth = { contacts: plan.contacts, total: plan.total, mode: plan.mode }
if (!quiet) {
process.stderr.write(
depth.mode === 'none'
? ` ${contactsText(depth.total)} contacts, the file's own: read as stored\n`
: ` ${depthPhrase(depth)}\n`,
)
}
return depth
}
/** A map opened for a run, with the facts an import carries that a mount does not. */
interface Opened {
mc: MetaCooler
source: ByteSource
/** The four orientation curves counted while binning a `.pairs`, or `null`. */
orientation: OrientationSummary | null
/** What `pairtools stats` counted in the same pass, or `null`. */
stats?: PairStats | null
/** Whether the map was binned from a `.pairs` here, rather than opened. */
binned?: boolean
}
/** `--bin-size` and `--rungs`, the CLI's answer to the browser's dialog. */
interface PairsBinning {
base: number
rungs: number
}
/**
* Open a file for a task, importing it first when it is a `.pairs`.
*
* The browser answers "at what resolution?" with a dialog; a shell answers it
* with a flag, and the refusal names the flag rather than describing a dialog
* nobody here can see. Everything after the open is identical, which is the
* point of GAPS G4: a number computed in a batch and a number computed by
* clicking come out of one implementation.
*
* The ladder is built even though a task reads one rung, and that is deliberate
* rather than wasteful — it costs a walk over the base pixel table, and it is
* what makes `--out` able to carry a `.mcool` that opens in the app at the same
* resolutions a session would have had.
*
* `uri` is what the map is called and `path` where its bytes are — one file
* for a path, the address itself for one read by range, and its downloaded
* copy for one fetched whole. A `.pairs` file's `.px2` is looked for beside it.
*/
async function openForTask(
uri: string,
source: ByteSource,
options: Pick<RunOptions, 'binning' | 'quiet' | 'downloads'>,
path: string,
): Promise<Opened> {
const named = parseUri(uri).path
try {
return { mc: await MetaCooler.open(uri, source), source, orientation: null }
} catch (error) {
if (!(error instanceof ViewerError) || error.code !== 'pairs-binning-needed') throw error
const binning = options.binning
if (binning === undefined) {
throw new ViewerError(
'pairs-binning-needed',
`${fileNameOf(named)} is a .pairs file: a list of contacts with no resolution of its own. ` +
'Say what to bin it at, e.g. `--bin-size 5000 --rungs 4`.',
error.detail,
)
}
const probe = await probePairs(source, () => openPairsIndex(path, options.downloads))
if (!options.quiet) {
const known = probe.records === null ? 'an unindexed file' : `${probe.records.toLocaleString()} records`
process.stderr.write(` binning ${known} at ${binning.base} bp\n`)
}
const imported = await importPairs(source, probe, {
base: binning.base,
rungs: binning.rungs,
...(options.quiet
? {}
: {
onProgress: (done, total, note) => {
if (total > 0 && done % Math.max(1, Math.floor(total / 10)) < 2) {
process.stderr.write(` ${note ?? 'working'} ${Math.round((done / total) * 100)}%\n`)
}
},
}),
})
if (imported === null) throw new Error('the pairs import was interrupted')
const pixels = imported.tables.get(imported.rungs[0])!
// The curves the pass just counted, as `worker/reader.worker.ts` hands them
// to the session: the records are gone once the table exists, and the task
// that draws them (`expected --stranded`) runs on the table.
const counted = pixels.orientation ?? null
return {
// …and its `pairtools stats`, for Pairs QC, which the session hands it the
// same way (`TaskInputs.pairsStats`).
stats: pixels.stats ?? null,
binned: true,
mc: MetaCooler.fromPairs({
uri: named,
header: imported.header,
pixels,
rungs: imported.rungs,
indexed: imported.indexed,
declaredRecords: imported.declaredRecords,
}),
source,
orientation:
counted === null
? null
: { edges: counted.edges, counts: counted.counts, total: counted.total },
}
}
}
/**
* The `.px2` beside a pairs file, on disk or at the address beside it, or `null`.
*
* Both spellings `pairix` writes, most specific first — the same rule
* `annotations/sidecar.ts` states for a `.bai`, and for the same reason: a
* reader must not have to know which convention produced the pair they have.
*/
async function openPairsIndex(path: string, downloads: Downloads): Promise<ByteSource | null> {
if (isAddress(path)) {
const name = fileNameOf(path)
for (const candidate of [`${name}.px2`, `${name.replace(/\.b?gz$/i, '')}.px2`]) {
const source = await downloads.sidecarRanged(path, candidate)
if (source !== null) return source
}
return null
}
for (const candidate of [`${path}.px2`, `${path.replace(/\.b?gz$/i, '')}.px2`]) {
if (!existsSync(candidate)) continue
try {
return await LocalFileSource.fromPath(candidate)
} catch {
return null
}
}
return null
}
/**
* Open a file named on the command line, by whichever road it needs.
*
* The browser's two roads (`worker/open.ts`), against a filesystem instead of a
* `SourceSpec`: an HDF5 container mounts, and a HiC-Pro matrix is read whole
* beside its bin file. Written here rather than reused wholesale because the
* discovery step is genuinely different — a path is `existsSync`, not a `HEAD`
* — but the parse below is the shared one, so a number computed in a shell and
* a number computed by clicking come out of the same implementation.
*
* An address is read **by range**, as the app reads it (§23.1): every road
* below but HiC-Pro's opens a byte source, and a range source is one. Where its
* host serves no range, and for a HiC-Pro matrix, which is read whole beside
* its bin file, it is fetched to disk by `cli/remote.ts` under the address's own
* file name, so every road that reads a name reads the one the reader typed.
* `keep` holds that copy to the end of the command — an `--against` every run
* reads — rather than letting it go once this run is done.
*/
async function openLocal(
uri: string,
options: Pick<RunOptions, 'binning' | 'quiet' | 'downloads'>,
keep = false,
): Promise<Opened> {
// **The `::` is addressed to the container, not to the filesystem.** An
// `.mcool` is a collection of coolers and `detect.ts` refuses one at its root
// with a sentence naming the resolutions and telling the reader to write
// `file.mcool::/resolutions/25000` — advice this shell then could not take,
// because the whole string went to `stat` and there is no such file. So the
// path is split off for the filesystem and the *uri* is what the container is
// opened with, which is where `parseUri` reads the group from.
const named = parseUri(uri).path
if (isAddress(named) && !isHicProMatrix(fileNameOf(named))) {
const ranged = await options.downloads.ranged(named)
if (ranged !== null) {
try {
return await openForTask(uri, ranged, options, named)
} catch (error) {
ranged.close()
throw error
}
}
}
const path = (await options.downloads.local(named, keep)) ?? named
const name = basename(path)
if (!isHicProMatrix(name)) {
// The HDF5 road, and the `.pairs` import that hangs off its one refusal.
const source = await LocalFileSource.fromPath(path)
return openForTask(uri, source, options, path)
}
const beside = hicProBinsNames(name)
.map((n) => join(dirname(path), n))
.find((candidate) => existsSync(candidate))
if (beside === undefined) {
throw new Error(
`${name} is a HiC-Pro matrix, which is half of a contact map: the bin file beside it — ` +
`${hicProBinsNames(name).join(' or ')} — is what says which genomic interval each bin ` +
`id means, and there are no coordinates without it.`,
)
}
const binBytes = await decodeWhole(readFileSync(beside))
const parsedBins = parseBins(binBytes, basename(beside))
const matrixBytes = await decodeWhole(readFileSync(path))
const opened = await hicProMap(
named,
{ bytes: matrixBytes, name },
parsedBins,
basename(beside),
binBytes.length,
)
return { ...opened, orientation: null }
}
/**
* One half of a HiC-Pro pair, read whole and un-gzipped if it is gzipped.
*
* Capped in proportion to the file rather than at the text ceiling, as the
* worker's own read of the pair is (`worker/sources.ts`): both halves are parsed
* from their bytes, and a matrix may be past a gigabyte (§3.9).
*/
function decodeWhole(read: Buffer): Promise<Uint8Array> {
const bytes = new Uint8Array(read)
return decodeAnnotationBytes(bytes, inflationCap(bytes.length, WHOLE_FILE_INFLATION))
}
/**
* One task, one file, one result — the CLI's whole unit of work.
*
* The `JobContext` here is the one `analysis/worker/analysis.worker.ts` builds,
* with the two differences a shell makes: nothing can be cancelled, so
* `cancelled` is constant, and progress goes to stderr rather than into a
* message. `breathe` still yields, because the runners call it in their outer
* loops and a promise that never resolves would hang.
*/
async function runOne(options: RunOptions): Promise<TaskResult & { contigs: BedGraphContig[] }> {
const { task, path } = options
options.downloads.refuseScheme(path)
const opened = await openLocal(uriOf(path), options)
let mc = opened.mc
try {
// The ticked cells, as the analysis worker selects them before any task
// runs: an `.scool` sums whichever cells are chosen, and a task over "the
// map" is a task over that sum (§3.8).
if (options.cells.length > 0) {
if (mc.cells.length === 0) {
throw new Error(`${fileNameOf(path)} has no cells to choose from; --cell is for an .scool.`)
}
mc.selectCells(options.cells)
}
// Drawn to the total asked for before anything reads it, as the analysis
// worker draws its mount (§6.5); the seed is the app's, so the pixels are.
const depth = await drawnTo(mc, options.contacts, options.quiet)
// At the resolution asked for, the file's bins summed (§3.4) — last, as the
// analysis worker sums its mount, so the cells and the total are summed.
const fileBinsize = mc.binsize
if (options.coarsen !== undefined) mc = atResolution(mc, options.coarsen, path)
const coarsened = mc.binsize !== fileBinsize
const value = options.value ?? DEFAULT_COUNT_COLUMN
if (value !== DEFAULT_COUNT_COLUMN && !mc.scoreColumns.includes(value)) {
throw new Error(
`${fileNameOf(path)} has no score column ${JSON.stringify(value)}. It has: ` +
`${mc.scoreColumns.join(', ') || DEFAULT_COUNT_COLUMN}.`,
)
}
// An origin on a sequence the file has not got, or past its end, is a
// typing mistake — refused by name rather than read as *no origin*.
for (const [name, at] of Object.entries(options.origins)) {
const id = mc.chromnames.indexOf(name)
if (id < 0) {
throw new Error(`--origin ${name}: ${fileNameOf(path)} has no sequence of that name.`)
}
const length = mc.coords.contigLengths[id]
if (at >= length) {
throw new Error(
`--origin ${name}:${(at + 1).toLocaleString('en-US')} is past its end, at ` +
`${length.toLocaleString('en-US')} bp.`,
)
}
}
// The window as a reader writes one — 1-based and inclusive, digits grouped
// or not, `IV:1,000,001-1,400,000` — which is what the console writes and
// what every locus box in the app reads (§26.1), and in cooler's grammar
// from here on. It used to be read in that grammar as typed, so the digits
// a reader copied off the app's own breadcrumb named a window starting one
// base later at a shell than on the screen they came from.
const region = options.window === undefined ? undefined : typedLocusToRegion(options.window)
const extent =
region === undefined
? ([0, mc.nBins] as [number, number])
: mc.extent(region)
const balance = options.balance ?? mc.hasWeights
const params = withDerived(task, options.params, balance)
const framing: AnalysisFraming = {
uri: mc.uri,
rows: extent,
cols: extent,
binsize: mc.binsize,
binsPerCell: 1,
balance,
value,
normalise: null,
level: 'bin',
label:
`${region === undefined ? 'whole file' : regionLabel(region)} at ${mc.binsize} bp` +
`${coarsened ? ` (${fileBinsize} bp bins summed)` : ''}` +
`${balance ? ', balanced' : ''}, ${value}` +
`${options.circular.length === 0 ? '' : `, circular ${options.circular.join(',')}`}` +
`${Object.keys(options.origins).length === 0 ? '' : `, origin ${originLabel(options.origins)}`}` +
`${options.cells.length === 0 ? '' : `, ${options.cells.length} cells`}` +
`${depth === null || depth.mode === 'none' ? '' : `, ${depthPhrase(depth)}`}`,
...(options.circular.length === 0 ? {} : { circular: [...options.circular] }),
...(Object.keys(options.origins).length === 0 ? {} : { origins: { ...options.origins } }),
...(options.contacts === undefined ? {} : { contacts: options.contacts }),
...(coarsened ? { coarsen: mc.binsize } : {}),
}
// The assembly travels with the result rather than being fetched again: a
// second open costs a second mount and a second metadata walk to learn
// something this one already knows.
const contigs: BedGraphContig[] = mc.chromnames.map((name, id) => {
const [startBin, endBin] = mc.coords.contigBinExtent(id)
return { name, startBin, bins: endBin - startBin, length: mc.coords.contigLengths[id] }
})
const notes: string[] = []
const started = Date.now()
let lastPercent = -1
const shared = {
cancelled: () => false,
throwIfCancelled: () => {
// Nothing can cancel a CLI run but Ctrl-C, which the process handles.
// Present so the runners' calls are not conditional on the venue.
void abortError
},
breathe: async () => {
await yieldToEventLoop()
},
progress: (done: number, total: number) => {
if (options.quiet || total <= 0) return
const percent = Math.floor((done / total) * 100)
// Only on a change, and only to stderr: a progress line interleaved with
// a TSV on stdout is a TSV nobody can pipe.
if (percent === lastPercent) return
lastPercent = percent
process.stderr.write(`\r ${task.title}: ${percent}% `)
},
note: (text: string) => {
notes.push(text)
},
}
const baseInputs: TaskInputs = {
...options.inputs,
contigLengths: Object.fromEntries(mc.chromsizes),
...(opened.orientation === null ? {} : { orientation: opened.orientation }),
// The records themselves, where the map was binned from them here: what
// their import counted, and the file again for a task that reads them
// (Pairs QC's fragments) — named as `peersOf` names a map, a path as a
// `file:` URL, and opened by `openSource` below.
...(opened.stats === undefined || opened.stats === null ? {} : { pairsStats: opened.stats }),
...(opened.binned === true ? { mapSource: specOf(path) } : {}),
// The map itself, by address, for the report that reads its finest rung:
// a path, or an address, with the group it was opened at.
...(opened.binned === true ? {} : { self: { label: fileNameOf(path), uri: path, source: specOf(path) } }),
...(options.peers.length === 0 ? {} : { peers: peersOf(options.peers) }),
// This map by its base name too, as `peersOf` names the others, so the
// matrix's axes and the tables name every file the same way.
...(options.peers.length === 0 ? {} : { mapLabel: fileNameOf(options.path) }),
}
/**
* The job for one step of the chain, built as `analysis.worker.ts` builds
* its own — with the capabilities a shell answers differently from a
* worker: `peer`, `openFile` and `openBytes` read the filesystem, an address
* once it is fetched, and `vectors` is computed here rather than asked of
* another thread.
*/
const jobFor = async (
step: AnalysisTask,
stepParams: Params,
upstream: Record<string, TaskResult>,
): Promise<JobContext> => ({
mc,
// Every locus in cooler's grammar, as the analysis worker is handed it
// (`runnerParams`); the provenance below keeps the one that was typed.
params: runnerParams(step.params, stepParams),
framing,
inputs: {
...baseInputs,
...(await vectorsFor(step, stepParams, options, { contigs, binsize: mc.binsize, nBins: mc.nBins })),
...(Object.keys(upstream).length === 0 ? {} : { upstream: { ...upstream } }),
},
...shared,
toBp: (bins) => bins * mc.binsize,
toBins: (bp) => Math.max(1, Math.round(bp / mc.binsize)),
// A second mount for the length of one run, closed by the runner: the
// analysis worker's own `peer`, against a filesystem instead of a
// `SourceSpec`. Mounted through `openLocal`, so a `.pairs` or a HiC-Pro
// pair beside the map opens by the same road the map did — and an address
// by range, or from the copy of one whose host serves none.
peer: async (map) => {
const other = await openLocal(uriOf(map.uri), options, true)
// Every map of a comparison at the one depth (§6.5).
try {
await drawnTo(other.mc, options.contacts, options.quiet)
} catch (error) {
other.mc.close()
other.source.close()
throw error
}
// …and at the one resolution where its bins sum to it (§3.4); where they
// do not, as it is, and the task says the two are at different ones.
let read = other.mc
if (options.coarsen !== undefined) {
try {
read = atResolution(other.mc, options.coarsen, map.uri)
} catch {
read = other.mc
}
}
return {
mc: read,
close: () => {
read.close()
other.source.close()
},
}
},
// A file this process can read and does not mount — a `.pairs` named for
// its orientation curves.
openFile: async (file) => {
// Mounted, because a path-backed source reads through the mount and
// refuses a range before one exists — and mounted rather than read
// whole, since a contact list is the one input here that is routinely
// larger than memory.
const source = await LocalFileSource.fromPath(resolve(file))
await source.mount()
return source
},
// The same, named by an address — read by range, as the worker reads
// it and as a map is read here, or from a copy where its host serves none.
openBytes: async (url) => openAddress(url, options.downloads),
// A file handed over as a `SourceSpec` — here only ever the map's own
// `.pairs`, as `specOf` spelled it: a path as a `file:` URL, read where it
// lies, or an address, read as `openBytes` reads one.
openSource: async (spec) => {
if (spec.kind !== 'remote') {
throw new Error('a file handed over in a browser cannot be read from a shell')
}
if (spec.url.startsWith('file:')) {
const source = await LocalFileSource.fromPath(fileURLToPath(spec.url))
await source.mount()
return source
}
return openAddress(spec.url, options.downloads)
},
})
const outputs = await runChain(task, params, framing, jobFor, options)
if (!options.quiet) process.stderr.write('\r')
return {
contigs,
outputs,
provenance: {
task: task.id,
taskVersion: task.version ?? 0,
params,
framing,
app: APP,
createdAt: new Date().toISOString(),
},
notes,
ms: Date.now() - started,
}
} finally {
mc.close()
}
}
/**
* The other maps, as the analysis worker is handed them.
*
* A `PeerMap` carries the reader's own name for a panel and a `SourceSpec` for
* the worker's mount cache; here the name is the file's and the spec is the
* path spelled as a URL — or the address, for one — which `peer` above never
* reads: it opens `uri`. The label is what the coefficient matrix's axes say,
* so it is the file's name and not the whole path a batch script would have
* expanded, nor an address's query.
*/
function peersOf(paths: readonly string[]): PeerMap[] {
return paths.map((path) => {
const file = parseUri(path).path
return {
label: fileNameOf(path),
uri: path,
source: { kind: 'remote', url: isAddress(file) ? file : pathToFileURL(resolve(file)).href },
}
})
}
/**
* The name a file is opened under: an address as it was typed, and a path
* made absolute, as the framing has always recorded one.
*/
function uriOf(path: string): string {
return isAddress(path) ? path.trim() : resolve(path)
}
/**
* A file named on the line as the `SourceSpec` a task is handed: an address as
* it is, and a path as the `file:` URL `peersOf` writes for one — which the job's
* own `openSource` reads back where it lies.
*/
function specOf(path: string): SourceSpec {
const file = parseUri(path).path
return { kind: 'remote', url: isAddress(file) ? file.trim() : pathToFileURL(resolve(file)).href }
}
/** An address opened for its bytes: by range, or from a copy where its host serves none. */
async function openAddress(url: string, downloads: Downloads): Promise<ByteSource> {
const where = await downloads.where(url, true)
const source = where.kind === 'range' ? where.source : await LocalFileSource.fromPath(where.path)
await source.mount()
return source
}
/**
* The per-bin vectors a task of the *analysis* venue reads a track or a
* sequence through (§18.6).
*
* `AnalysisRunner.inputsFor` asks the annotations worker for one vector per
* chosen entry of those two kinds and ships it under the parameter's key; the
* runner then reads `inputs.vectors[key]` and never learns a file was involved.
* A shell that loaded the FASTA under `--sequence` and never did this left
* `compartments --phaseSequence` reporting that the sequence *could not be
* read*, about a file the command had just parsed. So the same vector is
* computed here, from the loaded track or from the reference as a GC track.
*
* **Under the runner's own keys**, which is what {@link chosenEntries} is
* exported for, and both halves of that matter: a parameter that takes several
* entries files each under `key:entryId`, and it is a *list* rather than a
* string. Read as a single string, `apa --tracks signal.bw` chose nothing at
* all, and the pileup came back with the note that one of one tracks could not
* be read — about a file the command had just opened.
*/
async function vectorsFor(
task: AnalysisTask,
params: Params,
options: RunOptions,
grid: { contigs: readonly BedGraphContig[]; binsize: number; nBins: number },
): Promise<Pick<TaskInputs, 'vectors'>> {
if (task.venue === 'annotations') return {}
const vectors: Record<string, Float32Array> = {}
for (const spec of task.params) {
if (spec.kind !== 'track' && spec.kind !== 'sequence') continue
for (const [key, named] of chosenEntries(spec, params)) {
const track =
spec.kind === 'track'
? trackFor(options.tracks, named)
: gcTrackFor(options.sequences, named)
if (track === undefined) continue
vectors[key] = await vectorOver(track, {
contigs: grid.contigs.map((contig) => ({
name: contig.name,
startBin: contig.startBin,
length: contig.length,
})),
binsize: grid.binsize,
nBins: grid.nBins,
})
}
}
return Object.keys(vectors).length === 0 ? {} : { vectors }
}
/** A loaded reference as the GC track the session would have sampled it as. */
function gcTrackFor(
held: Map<string, Reference>,
entry: string,
): LoadedTrack | undefined {
const found = storeFor(held, entry)
return found === undefined ? undefined : gcTrack(found[0], fileNameOf(found[0]), found[1])
}
/**
* The task and everything it `requires`, required tasks first.
*
* `AnalysisRunner.plan`, without the cache: depth first, each requirement at
* its own defaults — the reader configured the network and not the QC under
* it, and inventing parameters for a form they never opened would be putting
* numbers in their mouth — except what the task's own flags answered for the
* step (`upstreamParams`: Pairs QC's `--sequence` and `--enzyme` are the
* restriction step's), laid over them, and a step the task says to leave out,
* which is not run at all. De-duplicated, so two steps wanting one upstream
* result compute it once. A cycle is a catalogue mistake and is named rather
* than run into.
*/
async function runChain(
task: AnalysisTask,
params: Params,
framing: AnalysisFraming,
jobFor: (
step: AnalysisTask,
stepParams: Params,
upstream: Record<string, TaskResult>,
) => Promise<JobContext>,
options: Pick<RunOptions, 'sequences' | 'tracks'>,
): Promise<TaskOutput[]> {
const upstream: Record<string, TaskResult> = {}
const active = new Set<string>()
const walk = async (node: AnalysisTask, nodeParams: Params): Promise<TaskOutput[]> => {
if (active.has(node.id)) throw new Error(`the analysis task ${node.id} requires itself`)
active.add(node.id)
for (const id of node.requires ?? []) {
if (id in upstream) continue
const required = taskById(id)
if (required === undefined) {
throw new Error(`${node.id} requires the task ${id}, which this build does not have`)
}
// What the task answered for the step, or that it is to be left out —
// `upstreamParamsOf`, the function `AnalysisRunner.plan` asks too.
const answered = upstreamParamsOf(node, id, nodeParams)
if (answered === null) continue
// Its own defaults under those answers, and balancing as the framing reads
// the file — which a required step's form would have set from the file too —
// unless the task answered it: the map report's library is the raw counts
// however the map is read, and `AnalysisRunner.plan` keeps that answer too.
const requiredParams = withDerived(
required,
Object.fromEntries(
Object.entries({ ...defaultParams(required.params), ...answered }).filter(
([key]) => key in answered || !required.params.some((spec) => spec.key === key && paramDerived(spec)),
),
),
framing.balance,
)
const started = Date.now()
const outputs = await walk(required, requiredParams)
upstream[id] = {
outputs,
provenance: {
task: required.id,
taskVersion: required.version ?? 0,
params: requiredParams,
framing,
app: APP,
createdAt: new Date().toISOString(),
},
notes: [],
ms: Date.now() - started,
}
}
active.delete(node.id)
return runFor(node, await jobFor(node, nodeParams, upstream), options)
}
return walk(task, params)
}
/**
* A task of the annotations venue, run with **no contact map** at all.
*
* The 1D browser (§5.8) is a session with tracks and an assembly and no
* matrix, and five tasks run there. `AnalysisRunner.tracksFraming` frames such
* a run against the file that declared the assembly, over a zero-wide extent —
* and the console recorded it as a sentence, because this command opened its
* first argument as a map and there was none to name. Now there need not be:
* with no positional, a track task runs over the assembly the loaded files
* declare, framed exactly as the session frames it, so the line the console
* writes for a browser run is a line this can take.
*/
async function runTracksOnly(
options: Omit<RunOptions, 'path'>,
): Promise<TaskResult & { contigs: BedGraphContig[] }> {
const { task, params } = options
const lengths = lengthsOf(options.tracks, options.sequences)
const named = [...options.tracks.values()][0]?.path ?? [...options.sequences.keys()][0] ?? ''
const framing: AnalysisFraming = {
uri: named,
rows: [0, 0],
cols: [0, 0],
binsize: 0,
binsPerCell: 1,
balance: false,
value: 'count',
normalise: null,
level: 'bin',
label:
`${fileNameOf(named)} · ${task.mapless === true ? 'sequences' : 'loaded tracks'}, no contact map` +
`${options.circular.length === 0 ? '' : `, circular ${options.circular.join(',')}`}` +
`${Object.keys(options.origins).length === 0 ? '' : `, origin ${originLabel(options.origins)}`}`,
// A task on the sequence reads what the molecules are as surely as one on
// the map (§8.15): an origin call on a circle read as a line splits an
// origin at the first base between the two ends.
...(options.circular.length === 0 ? {} : { circular: [...options.circular] }),
...(Object.keys(options.origins).length === 0 ? {} : { origins: { ...options.origins } }),
}
const notes: string[] = []
const started = Date.now()
let lastPercent = -1
const job: TrackJobContext = {
params: runnerParams(task.params, params),
framing,
inputs: { ...options.inputs, contigLengths: lengths },
cancelled: () => false,
throwIfCancelled: () => {
void abortError
},
progress: (done, total) => {
if (options.quiet || total <= 0) return
const percent = Math.floor((done / total) * 100)
if (percent === lastPercent) return
lastPercent = percent
process.stderr.write(`\r ${task.title}: ${percent}% `)
},
note: (text) => {
notes.push(text)
},
sample: samplerOver(options.tracks),
lengthOf: (contig) => lengths[contig],
residues: (entry) => readerFor(options.sequences, entry),
}
const runner = TRACK_RUNNERS[task.id]
if (runner === undefined) {
throw new Error(`no analysis runner is registered for the task ${task.id}`)
}
const outputs = await runner(job)
if (!options.quiet) process.stderr.write('\r')
// No map, so no grid of its own: the one profile that can come out of this —
// base composition's, on bins it picked (§18.8) — is written over these
// sequences cut at its bin size, and a BED against the right names.
const contigs: BedGraphContig[] = Object.entries(lengths).map(([name, length]) => ({
name,
startBin: 0,
bins: 0,
length,
}))
return {
contigs,
outputs,
provenance: {
task: task.id,
taskVersion: task.version ?? 0,
params,
framing,
app: APP,
createdAt: new Date().toISOString(),
},
notes,
ms: Date.now() - started,
}
}
// ---------------------------------------------------------------------------
// The other venue
// ---------------------------------------------------------------------------
/**
* Hand the job to whichever map holds this task's runner.
*
* A task declares the worker it belongs in and there are two of them
* (`analysis/job.ts`), so there are two runner maps and this is the only place
* that has to know it. Dispatching on `task.venue` rather than on which map
* happens to answer is deliberate: the venue is the fact the descriptor states,
* and a task present in both maps under one id would be a build error worth
* failing on rather than a coin toss resolved by lookup order.
*
* A shell can be either venue, which is what the split does *not* say and what
* this is allowed to exploit. The annotations worker earns its own context by
* holding open bigWig handles and a parsed genome; the reason a task runs beside
* them is that the data must not be shipped, and nothing is shipped here — the
* store, the runner and the writer are one stack in one process.
*/
async function runFor(
task: AnalysisTask,
job: JobContext,
loaded: Pick<RunOptions, 'sequences' | 'tracks'>,
): Promise<TaskOutput[]> {
if (task.venue === 'annotations') {
const runner = TRACK_RUNNERS[task.id]
if (runner === undefined) {
throw new Error(`no analysis runner is registered for the task ${task.id}`)
}
return runner(trackJobOf(job, loaded))
}
const runner = RUNNERS[task.id]
if (runner === undefined) {
throw new Error(`no analysis runner is registered for the task ${task.id}`)
}
return runner(job)
}
/**
* The same job, seen from the annotations venue.
*
* `analysis/job.ts` says what the two contexts share — parameters, framing,
* inputs, cancellation, progress and notes — and this is that sentence as code:
* each of those is the very function the map venue was handed, not a second one
* built from the same ingredients, so the two cannot come to differ in this
* file. What is added is the pair of capabilities that venue exists for:
* residues are a reference this process parsed, and a sample is answered from
* a track it opened (`cli/tracks.ts`), in the worker's own shape.
*/
function trackJobOf(
job: JobContext,
loaded: Pick<RunOptions, 'sequences' | 'tracks'>,
): TrackJobContext {
return {
params: job.params,
framing: job.framing,
inputs: job.inputs,
cancelled: job.cancelled,
throwIfCancelled: job.throwIfCancelled,
progress: job.progress,
note: job.note,
sample: samplerOver(loaded.tracks),
// Exactly the annotations worker's own answer: the assembly is what
// `inputs.contigLengths` carries, because this venue is handed no other.
lengthOf: (contig) => job.inputs.contigLengths?.[contig],
residues: (entry) => readerFor(loaded.sequences, entry),
}
}
/**
* A loaded reference, by whatever name the `sequence` parameter holds.
*
* Three steps, because the parameter arrives by three roads. Typed on the
* command line it is a **path**, and that is the key `loadSequences` filed it
* under. Recorded in a workspace it is an **entry id** — `a3` — allocated by a
* store this process does not have, which is the absence `bindInputs` is a
* whole paragraph about; so a replay that named one reference gets that one,
* there being nothing else it could have meant. Two references and an id that
* matches neither is genuinely ambiguous and answers `undefined`, which
* `analysis/run/motif.ts` turns into a sentence rather than a guess.
*/
function readerFor(
held: Map<string, Reference>,
entry: string,
): SequenceReader | undefined {
const store = storeFor(held, entry)?.[1]
if (store === undefined) return undefined
// The worker's reader, step for step: `bases` by the §5.9 ladder, because a
// FASTA writes `chrI` where a `.hic` beside it writes `I` and a search under
// the map's spelling has to reach the reference's — and `read` beside it for
// a reference opened by range, which the motif search walks a piece at a
// time (`cli/reference.ts`).
return {
contigs: store.contigs,
bases: (contig) => store.bases(contig),
...(store.read === undefined ? {} : { read: store.read.bind(store) }),
}
}
/** The loaded reference an entry names, with the path it was filed under. */
function storeFor(
held: Map<string, Reference>,
entry: string,
): [string, Reference] | undefined {
const direct = held.get(entry)
if (direct !== undefined) return [entry, direct]
return (
[...held].find(([path]) => fileNameOf(path) === fileNameOf(entry)) ??
(held.size === 1 ? [...held][0] : undefined)
)
}
// ---------------------------------------------------------------------------
// Writing what came back
// ---------------------------------------------------------------------------
/**
* Every output, in every format that means anything for its kind.
*
* The same rule §18.7 states for the drawer — *bigWig for a signal, bedGraph,
* BED, TSV* — and the same writers, so a file produced here and a file produced
* by clicking are byte-identical given the same inputs. That is worth more than
* it sounds: it means a figure made in the browser and a table made in a batch
* can be compared without anybody wondering whether the difference is the tool.
*
* `earlier` is every file this command has written so far, and none of them is
* written over. The stems are made unique before the first run ({@link
* stemsOf}), so this is the floor under that rather than the rule: a second run
* replacing the first one's tables with exit 0 is a batch whose every result
* looks fine and half of which is missing.
*/
async function writeOutputs(
result: TaskResult,
base: string,
directory: string,
contigs: readonly BedGraphContig[],
quiet: boolean,
earlier: Set<string>,
): Promise<string[]> {
await mkdir(directory, { recursive: true })
const written: string[] = []
// A text file as its pieces, written as they are made: a profile at a fine
// bin size is more text than one string can hold (`write/tsv.ts`'s `pieces`).
const put = async (name: string, body: string | Iterable<string> | Uint8Array): Promise<void> => {
const at = join(directory, name)
// Without case, as a Mac's disk and Windows' compare names.
const key = resolve(at).toLowerCase()
if (earlier.has(key)) {
throw new Error(`${at} was written earlier by this command, and is not written over.`)
}
await writeFile(at, body)
earlier.add(key)
written.push(at)
if (!quiet) process.stderr.write(` wrote ${at}\n`)
}
for (const output of result.outputs) {
const stem = `${base}.${result.provenance.task}.${output.id}`
await put(`${stem}.tsv`, outputToTsv(output, result.provenance))
// The same rule as the drawer's, which has carried a BED button beside every
// called interval set since there were any: a profile leaves as bedGraph and
// bigWig, a set of intervals leaves as BED. Only the first half was here, so
// a boundary set called in a shell came out as a TSV with a provenance
// header — readable, and not what bedtools takes.
//
// **A model leaves as a bed3d** (§25.7), and the road a computed row shares
// with called intervals is this one too. A reconstruction's rows carry three
// coordinates each and BED6 has nowhere to put them: `reconstruct3d --out`
// wrote `chrom start end region_1 0 .` per bin — the assembly back, and the
// only thing the run computed gone — beside a TSV whose every row was blank.
// The writer is the drawer's own, so the file a batch produces is the file
// its button produces, and §25.2 reads it back.
if (output.kind === 'intervals') {
const payload = output.payload
const model = output.entryKind === 'structure' && payload.kind === 'features'
const context = {
label: output.label,
file: result.provenance.framing.label,
created: result.provenance.createdAt,
}
await put(
`${stem}.${model ? 'bed3d' : payload.kind === 'pairs' ? 'bedpe' : 'bed'}`,
model && payload.kind === 'features'
? writeBed3d(payload.data, context)
: formatIntervals(payload, context),
)
// And as a PDB beside it, for PyMOL, as the drawer and the Structures card
// offer one (§25.7) — except where the format's columns cannot number the
// model, which is said rather than skipped: a batch that silently wrote
// one file fewer is a folder somebody finds short a week later.
if (model && payload.kind === 'features') {
const refusal = pdbRefusal(payload.data)
if (refusal === null) await put(`${stem}.pdb`, writePdb(payload.data, context))
else if (!quiet) process.stderr.write(` no PDB for ${stem}: ${refusal}\n`)
}
}
if (output.kind === 'profile') {
// Over the grid the values are on: the map's, for every task that reads at
// its resolution, and the same sequences cut at the output's own bin size
// for the one that picks its own (§18.8) — which is also the only grid
// there is with no map named.
const grid =
output.binsize === result.provenance.framing.binsize ? contigs : gridAt(contigs, output.binsize)
await put(`${stem}.bedGraph`, profileToBedGraph(output, grid, result.provenance))
// The same three arguments the drawer's own bigWig button passes, so the
// two writers cannot drift: one implementation, one byte layout, one set
// of round-trip tests behind it.
//
// Deflated by Node's own zlib, synchronously: the bytes `CompressionStream`
// makes, without a stream a block (`BigWigWriting`).
const blob = await writeBigWig(
{
contigs: grid.map((contig) => ({ name: contig.name, length: contig.length })),
values: output.values,
firstBin: output.extent[0],
binsize: output.binsize,
},
{ deflate: (bytes) => deflateSync(bytes) },
)
await put(`${stem}.bw`, new Uint8Array(await blob.arrayBuffer()))
}
}
// **The run as a whole**, where the task leaves it so (§18.7): the map
// report's page, and the sections a pipeline's MultiQC collects by their
// `_mqc` suffix — each named after the file, which is the sample MultiQC
// reports it under.
for (const document of taskById(result.provenance.task)?.documents ?? []) {
await put(`${base}.${result.provenance.task}.${document.id}.${document.extension}`, document.write(result, base))
}
return written
}
// ---------------------------------------------------------------------------
// Inputs a task may need
// ---------------------------------------------------------------------------
/**
* One file named with `--features`, read as the app's loader reads it (§8).
*
* The worker's text road, in its order and through its parsers, as far as that
* road ends in a feature set or a pair set — so a file the browser draws as a
* gene model, a loop set or a karyotype reaches a task run from a shell as the
* same thing. Every format here is asked before `sniffFormat` for the worker's
* reason (§8.17): that function's last line is `return 'bed'`, so a format it
* has not been taught is never refused, only read as a BED, and here that was
* quiet. A genePred, a GTF and a VCF came out as nothing, each having a word
* where a BED has its start or its end; an interact as one box spanning both
* its anchors, or as a bedpe of the wrong columns; and a longrange as a BED4
* whose names were its arcs.
*/
export function readFeatureText(
text: string,
path: string,
): { features: FeatureSet } | { pairs: PairSet } {
// Called variants (§8.14), first as in the worker: eight columns or more,
// with a variant's ID where a BED has its end, so nothing below can take one
// and it can take nothing below.
if (sniffVcf(text)) return { features: parseVcf(text) }
// Asked before `sniffFormat` for the reason the worker asks it there
// (§8.17): the BED sniffer never answers "not one of mine", so a barChart
// read here as a BED would reach a task as intervals with no chart on them
// — which is fine for a metaplot and silently wrong for anything that reads
// the vector.
if (sniffBarChart(text, path)) return { features: parseBarChart(text, path) }
// A karyotype's bands, scored by how dark each stains (§8.22): read as a
// BED they kept their spans and lost the one column a task splitting light
// from dark bands would read.
if (sniffCytoBand(text)) return { features: parseCytoBand(text) }
// Introns, whatever shape the aligner wrote them in (§8.23). A STAR table
// read as a BED is intervals one base too wide with no count on them.
if (sniffJunctions(text, path) !== null) return { features: parseJunctions(text, path) }
// A model — the bed3d `reconstruct3d` writes, or a text g3d — is a set whose
// rows carry coordinates, which is what the structure tasks read (§25). Read
// as a BED it kept its intervals and lost the model, and Spatial tracks said
// the row it had just been handed was not a structure. A PDB first, by its
// name or its records: one this app wrote reads back as its model, and any
// other is refused with the reason rather than read as a BED of nonsense.
if (sniffPdb(text, path)) return { features: parsePdb(text, path) }
if (sniffBed3d(text, path)) return { features: parseBed3d(text, path) }
if (sniffG3d(text, path)) return { features: parseG3d(text, path) }
// UCSC's two interaction formats and its gene-model tables (§8.18, §8.19),
// in the worker's order, which matters nowhere since none can take another's
// file. An interact and a longrange are loop sets — a `PairSet`, as a bedpe
// is — and a genePred is transcripts with their exons, as a GTF's are.
if (sniffInteract(text, path)) return { pairs: parseInteract(text) }
if (sniffLongRange(text, path)) return { pairs: parseLongRange(text) }
if (sniffGenePred(text, path)) return { features: parseGenePred(text) }
const format = sniffFormat(text, path)
if (format === 'bedpe') return { pairs: parseBedpe(text) }
if (format === 'gtf') return { features: parseGtf(text) }
return { features: parseBed(text, path) }
}
/**
* One file named with `--pairs`: a loop table in whichever of the three paired
* formats it is written (§8.18).
*
* A bedpe unless its bytes say interact or longrange. The flag has already said
* what the file is for, so a bedpe the BED sniffer would not recognise — an
* Ensembl genome's, whose second contig is called `1` — is still read as one,
* as it always was here.
*/
export function readPairText(text: string, path: string): PairSet {
if (sniffInteract(text, path)) return parseInteract(text)
if (sniffLongRange(text, path)) return parseLongRange(text)
return parseBedpe(text)
}
/**
* Feature and pair sets named on the command line.
*
* Parsed by the app's own parsers, so a loop table the browser accepts is a loop
* table this accepts — including the headed TSV that most callers actually emit,
* which is the case `annotations/parse.ts` exists to get right.
*
* Keyed by the *file's base name* rather than by an entry id, because there is
* no store here to allocate one from and a name is what a reader would use to
* refer to it anyway. The same name goes into `labels`, so a correlation
* heatmap's axes read as filenames rather than as `a1`. An address is fetched
* first and named by its file, query and all left off.
*/
async function loadInputs(
args: Args,
downloads: Downloads,
task?: AnalysisTask,
): Promise<TaskInputs> {
const inputs: TaskInputs = {}
const labels: Record<string, string> = {}
for (const path of all(args, 'features')) {
const at = (await downloads.local(path, true)) ?? path
const text = await decodeAnnotationText(new Uint8Array(await readFile(at)))
const id = fileNameOf(path)
const read = readFeatureText(text, at)
if ('pairs' in read) inputs.pairs = { ...inputs.pairs, [id]: read.pairs }
else inputs.features = { ...inputs.features, [id]: read.features }
labels[id] = id
}
// **Not where the task claims the name for a contact list** — Pairs QC's
// `--pairs` is the `.pairs` its records are read from, one name and one
// meaning as `--window` is apa's. Read here as a loop table, a contact list
// of gigabytes was fetched whole and parsed as a BEDPE before anything ran.
const claimed = task?.params.some((spec) => spec.key === 'pairs' && spec.kind === 'file') === true
for (const path of claimed ? [] : all(args, 'pairs')) {
const at = (await downloads.local(path, true)) ?? path
const text = await decodeAnnotationText(new Uint8Array(await readFile(at)))
const id = fileNameOf(path)
inputs.pairs = { ...inputs.pairs, [id]: readPairText(text, at) }
labels[id] = id
}
if (Object.keys(labels).length > 0) inputs.labels = labels
return inputs
}
/**
* References named with `--sequence`, opened where they lie.
*
* {@link SequenceReader} is declared optional on its context precisely because
* the hosts that can answer it are *"the annotations worker"* and not *"a test
* harness, a future venue, or a session that has never opened a FASTA"*
* (`analysis/job.ts`). This is that future venue: the same parser the worker
* runs, over bytes read from the disk the file is already on — and, for a
* FASTA with its `.fai` beside it or a `.2bit`, the same arithmetic the worker
* reads by range with, so a mammalian genome is a reference here as it is in
* the browser (`cli/reference.ts`).
*
* Keyed by the string the reader typed, because that string is what comes back
* out of `params.sequence` — there is no entry store here to allocate an id
* from, which is the same absence `bindInputs` argues about at length. An
* address is read by range where it is, with the `.fai` beside it where the
* server has one, so a remote genome is never fetched whole for a window.
*/
async function loadSequences(
args: Args,
downloads: Downloads,
also: readonly string[] = [],
): Promise<Map<string, Reference>> {
const held = new Map<string, Reference>()
for (const path of [...all(args, 'sequence'), ...also]) {
if (held.has(path)) continue
const where = await downloads.where(path, true, SIDE_CACHE_BYTES)
held.set(path, await openReference(where, (name) => downloads.sidecarText(path, name)))
}
return held
}
/**
* The reference a task's own flag names that `--sequence` did not load, as a
* list of none or one.
*
* What a parameter names is what is loaded, which is `--tracks`' arrangement:
* `pairsqc --reference ref.fa` reads the file it names rather than running with
* no digest and a note saying the reference was never opened. Only for the
* parameter `--sequence` answers by itself ({@link referenceKeyOf}), the one a
* task hands on to the step it requires.
*/
function referenceNamed(task: AnalysisTask, params: Params): string[] {
const key = referenceKeyOf(task)
if (key === null || key === 'sequence') return []
const value = params[key]
// A path that is there, or an address: a workspace's entry id (`a3`) names no
// file, and is resolved against what `--sequence` loaded instead (`storeFor`).
return typeof value === 'string' && value !== '' && (isAddress(value) || existsSync(value)) ? [value] : []
}
/**
* A task's reference answered by the one `--sequence` the line loaded, where
* its own flag left it open.
*
* Pairs QC's `reference` is the restriction step's `sequence`, handed on
* (`upstreamParams`), so a line spells it as that step does: `pairsqc
* sample.pairs.gz --sequence ref.fa --enzyme DpnII`, which is the line the
* console writes (`analysis/cliCommand.ts`'s `referenceKeyOf`, the rule both
* sides read). Motif's is called `sequence` and is answered by the flag's own
* name already; two references loaded is two answers, and neither is guessed.
*/
function withReference(
task: AnalysisTask,
params: Params,
sequences: ReadonlyMap<string, Reference>,
): Params {
const key = referenceKeyOf(task)
if (key === null || key === 'sequence' || sequences.size !== 1) return params
const held = params[key]
if (typeof held === 'string' && held !== '') return params
return { ...params, [key]: [...sequences.keys()][0] }
}
/**
* Tracks named on the command line, by both roads a name arrives.
*
* A task's own `--tracks` is the path of a file to open, so a direct run needs
* no second flag: what the parameter names is what is loaded, which is the
* arrangement `--sequence` and `motif` already have. `--track` is the other
* road, for `replay`, where the parameter holds the app's entry id and the file
* has to be named beside it. A workspace also records what each id *was* — the
* tab's own track list, name and all — so an id is filed against the loaded
* file of that name and the recorded parameters resolve without anybody
* retyping them, which is the whole point of `replay`.
*
* Opened before any map, so an unreadable track is exit 2 with a sentence
* rather than the same failure once per file — and so is a name that looks like
* a path and is not one. An address is opened then too — a bigWig or a `.2bit`
* by range, a text track in one request — and filed under the address it was
* named by.
*/
async function loadTrackFiles(
tasks: readonly { task: AnalysisTask; params: Params }[],
args: Args,
downloads: Downloads,
stored: readonly StoredEntry[] = [],
): Promise<Map<string, LoadedTrack>> {
const paths: string[] = [...all(args, 'track')]
const unresolved: string[] = []
for (const { task, params } of tasks) {
for (const spec of task.params) {
if (spec.kind !== 'track') continue
const chosen = params[spec.key]
const named = Array.isArray(chosen)
? chosen.filter((item): item is string => typeof item === 'string')
: typeof chosen === 'string' && chosen !== ''
? [chosen]
: []
for (const path of named) {
if (isAddress(path) || existsSync(path)) paths.push(path)
else unresolved.push(path)
}
}
}
const held = await loadTracks(paths, (path) => downloads.where(path, true, SIDE_CACHE_BYTES))
// The app's ids, filed against the files they named: `a1` was `signal.bw`
// when the workspace was saved, and `--track signal.bw` is on the line.
for (const entry of stored) {
if (entry.kind !== 'track' || held.has(entry.id)) continue
const name = fileNameOf(entry.source.url ?? entry.source.name)
const match = [...held.values()].find((track) => track.name === name)
if (match !== undefined) held.set(entry.id, match)
}
for (const name of unresolved) {
if (trackFor(held, name) !== undefined) continue
throw new Error(
/[./\\]/.test(name)
? `--tracks names ${name}, which is not there.`
: `${name} is a track the workspace recorded by the app's own id. Name the file ` +
'with --track <file>.',
)
}
return held
}
/**
* What each loaded track is **called**, beside the labels the sets carry.
*
* A figure's axis reads `inputs.labels[entry]` and falls back to the entry
* itself, which here is the path as typed — so a correlation matrix's axes
* read as `/data/run3/signal.bw` until this says what they are. And what they
* are is what the app calls the same file once it is dropped: `signal`, its
* row's label (`annotations/names.ts`). The base name, `signal.bw`, was what
* this said until the two were run side by side (`notebooks/parity.qmd`): a
* metaplot's columns, a correlation's axes and FRiP's rows then named one
* track two ways, and a table from the shell could not be laid beside the
* drawer's by its headers.
*/
function withTrackLabels(inputs: TaskInputs, tracks: ReadonlyMap<string, LoadedTrack>): TaskInputs {
if (tracks.size === 0) return inputs
const labels: Record<string, string> = { ...inputs.labels }
for (const [key, track] of tracks) labels[key] = cleanLabel(track.name)
return { ...inputs, labels }
}
/**
* What each loaded reference is called: its file name, as a track's is.
*
* The tasks that read one name their outputs after it — *GC content · PAK.fa*,
* the name the app's own entry has — and fall back to the word *reference*
* where the label is missing, which here it always was.
*/
function withSequenceLabels(
inputs: TaskInputs,
sequences: ReadonlyMap<string, Reference>,
): TaskInputs {
if (sequences.size === 0) return inputs
const labels: Record<string, string> = { ...inputs.labels }
for (const path of sequences.keys()) labels[path] = fileNameOf(path)
return { ...inputs, labels }
}
/**
* File each loaded set under the **parameter key** that chose it.
*
* {@link TaskInputs} is keyed by parameter key — `analysis/job.ts`'s
* `chosenInput` is a whole paragraph about not indexing it by the entry id —
* and this side had been filing everything by file name and then setting the
* parameter to a *path*. The two never met: every task that takes a feature or
* pair set found `undefined` under its own key and reported "the set chosen is
* no longer loaded" about a file it had just parsed. It type-checks, it reads
* as though it must work, and it is the exact mistake that function exists to
* stop, made from the one venue that has no store to allocate ids in.
*
* So the name a reader typed still names the input, and the parameter key is an
* alias for it. Both, because `labels` is keyed by the first and the runners
* look up the second.
*/
function bindInputs(task: AnalysisTask, params: Params, inputs: TaskInputs): TaskInputs {
const bound: TaskInputs = { ...inputs }
for (const spec of task.params) {
if (spec.kind !== 'featureSet' && spec.kind !== 'pairSet') continue
const chosen = params[spec.key]
if (typeof chosen !== 'string' || chosen === '') continue
const name = fileNameOf(chosen)
if (spec.kind === 'pairSet') {
const set = inputs.pairs?.[chosen] ?? inputs.pairs?.[name]
if (set !== undefined) bound.pairs = { ...bound.pairs, [spec.key]: set }
} else {
const set = inputs.features?.[chosen] ?? inputs.features?.[name]
if (set !== undefined) bound.features = { ...bound.features, [spec.key]: set }
}
}
return bound
}
// ---------------------------------------------------------------------------
// Commands
// ---------------------------------------------------------------------------
/**
* What `--help` prints. Exported for the command-line page the site serves to
* language models (`llms/cli.ts`), which carries it whole rather than a
* paraphrase of it.
*/
export const USAGE = `chromosomix — the Analysis panel, from a shell
chromosomix tasks [--json]
Every task, its id, and the parameters it takes. With --json, the same
as one JSON document: every value a choice takes, every range and unit,
what each input reads and what each task writes.
chromosomix <task> <file.cool|file.mcool|file.metacool|file.hic|file.pairs.gz> [...]
Run one task over one or more files. Each file's outputs are named after
it, up to its first dot: sample.coverage.coverage-total.tsv. Two files
that would share a name keep more of theirs — HCT116.rep1 and
HCT116.rep2, then dirA_sample and dirB_sample — and nothing one command
writes is written over by it.
--out <dir> where to write (default: .)
--window <chr:a-b> a window rather than the whole file, 1-based and
inclusive as the app, IGV and samtools write it,
digits grouped or not: chrIV:1,000,001-1,400,000
--no-balance read the raw counts. A map is read balanced wherever
the file carries weights, as the app reads it
--features <file> a feature or loop file a task needs, read as the app
reads it: BED, narrowPeak, GTF, genePred, VCF,
cytoBand, barChart, junctions, bedpe, interact,
longrange
--sequence <ref.fa> a reference, for a task that reads residues (motif,
restriction, and pairsqc's digest) or phases by GC
content (compartments). Gzipped or not; read by
range where its .fai is beside it, or a .2bit
--pairs <file> a BEDPE, interact or longrange, for an off-diagonal
pileup. Note this is a *feature* table and not a
contact list — a .pairs file to bin is a positional
argument, and takes --bin-size below. pairsqc's own
--pairs is the exception: the contact list a matrix
was made from, read for its records
--against <file> another contact map, for a task that compares two
(hicrep). Repeat it for a third
--value <column> the score column to read, for a file that carries
more than the count (default: count)
--origin <name:pos> where a sequence's replication origin is, 1-based,
as the Origin and terminus task reports it; repeat
or separate with commas
--circular <name> a sequence to read as a circle (a plasmid); repeat
or separate with commas
--cell <name> a cell of an .scool to sum into the map; repeat or
separate with commas. Default: every cell
--contacts <n> draw the map to n contacts before the task reads it:
below the file's own total, an exact subsample
(cooltools random-sample --count n --exact); above
it, an oversample through Boost-HiC. Takes 10M,
23,000,000 or 2.5e7; --against maps are drawn to it
too. The same seed as the app, so the same pixels
--coarsen <bp> read the map at this bin size, a whole number of the
file's own bins summed along each sequence — what
the app does at a resolution you added (3 kb*).
Counts sum exactly; a bin's weight is the harmonic
mean of its bins' weights. --against maps are summed
to it too
--bin-size <bp> required for a .pairs input, which states no
resolution of its own; ignored for every other format
--rungs <n> how many ladder resolutions to build from it
(1-2-5 series from the base). Default 1
--threads <n> threads for a task that shares its work —
pastis-NB's MDS start and likelihood in
reconstruct3d. Default 1, so a time is one core's;
the results are the same bits on any number
--quiet no progress on stderr
--<param> <value> any parameter the task takes; see \`tasks\`. A choice
is one of its values and a number is a number: any
other is refused before a file is opened, with the
values it takes. A locus (fourc's --anchor, the 3D
tasks' --region and --locus) is read as --window is.
A task that reads tracks (metaplot, trackcorr, frip,
groupsignal) takes them as --tracks <file.bw>,
repeated or comma-separated: a bigWig, a bedGraph, a
wig, or a FASTA read as GC content
--<switch> a parameter that is on or off, which takes no value
after it: --derivative turns one on, and
--derivative=false or --no-derivative turns it off
chromosomix <task> --tracks <file.bw> --features <file.bed> [...]
A task that reads tracks and no matrix (metaplot, trackcorr, frip,
groupsignal, overlap, motif, composition, oriter), run with no contact map
at all — what a 1D browser session runs. The assembly is what the tracks
and references declare.
chromosomix circular <file.mcool::/resolutions/<bp>> [...]
Which sequences join their own ends: the junction test the app runs when
a map is first opened, as a table on stdout — sequence, length, score,
and yes or no where it could be decided: a sequence needs 50 bins at the
resolution read. The names to hand every other run as --circular.
chromosomix boost <file.mcool::/resolutions/<bp>> [...]
The boosted map of each sequence: what an oversample (--contacts above
the file's own total) draws the sequence's new contacts from — the bins
the outlier filter keeps, and the boosted map over them in SCN units.
One square TSV per sequence, rows and columns named by each kept bin's
start, into --out.
--sequences <a,b> the sequences to boost. Default: every one; a
sequence past 3,000 bins is refused by name
--alpha <a> the exponent of the distances, 1/SCN^a.
Default: 0.2
chromosomix stats <file.pairs.gz> [...]
What \`pairtools stats\` writes for a .pairs file, counted by the pass the
app's import makes: records mapped on both sides, on one and on neither,
duplicates, cis and trans and cis past 1 to 40 kb, every pair type, the
four orientations by separation and where they converge, and the
library's size. One <name>.stats per file into --out, in pairtools' own
format, which MultiQC and \`pairtools stats --merge\` read; to stdout
without --out.
chromosomix replay <workspace.chromosomix.json> --over <file> [...]
Re-run every analysis recorded in a saved workspace, with the parameters
it recorded, over the files named by --over and after the workspace —
--over data/*.hic as a shell expands it. The workspace is what the
app's Save button produces: every open tab in one file. A locus it
recorded is read as --window is, as the app's form showed it; a value
it recorded that this build cannot run is refused, before any file is.
--tab <n> which tab to replay, 1-based. Default: the one that
was in front when the workspace was saved.
--track <file.bw> the file behind a track the workspace recorded by
the app's own id. Repeat it per track
--against <file> the other maps a recorded hicrep compared against
chromosomix --version
Which build this is: chromosomix, its version and the commit it was
built from, on the first line, as every file it writes opens with them.
Then what the version does not fix — the Node it runs on, and the
h5wasm and @gmod/bbi installed beside it, which read every map and track.
A file may be an http or https address — a map, or what --against,
--sequence, --tracks, --features or --pairs names. A map, a bigWig, a .2bit
and an indexed FASTA are read by range, as the app reads them, and nothing of
them is written to disk. What is read whole — a feature file, a HiC-Pro
matrix, a workspace, or any file whose host serves no range — is fetched into
$TMPDIR, with its progress on stderr, and removed when the command ends.
Every task, what it reads and writes, and how to read a result:
${DOCS_URL}
`
/**
* What `--version` prints: which build this is, and what it is running on.
*
* The first line is the name and the version, with the commit the bundle was
* built from where it was built in a repository — the words every file the
* command writes opens with (`# chromosomix 0.13.0 cli`), so `head -1` is the
* line a pipeline records and a methods section cites.
*
* The rest is what a version does not fix. The Node the command runs on, with
* its platform; and the two libraries every map and every track is read
* through, `h5wasm` — which is HDF5 — and `@gmod/bbi`. Both are ranges in
* `package.json`, settled when the package is installed rather than when it was
* built, so two installs of one version can read a file through two builds of
* either; which is why their numbers are read off the copies installed beside
* this file, and not baked in. npm is not among them: it installs the command
* and takes no part in a run.
*/
function versionText(): string {
const lines = [
`chromosomix ${VERSION}${COMMIT === '' ? '' : ` (${COMMIT})`}`,
`node ${process.versions.node} on ${process.platform}-${process.arch}`,
...['h5wasm', '@gmod/bbi'].map((name) => `${name} ${installedVersion(name) ?? '(not found)'}`),
]
return `${lines.join('\n')}\n`
}
/**
* The version of `name` as installed where this file imports it from, or
* `undefined` where it is not.
*
* Node's own walk for a bare specifier — `node_modules/` beside this file and
* beside every directory above it — rather than `require.resolve`, which both
* packages refuse: each exports an `import` condition alone, and neither
* exports its `package.json`. The walk finds the copy a global install nests
* under the package and the one `npx` hoists beside it alike.
*/
function installedVersion(name: string): string | undefined {
let directory = dirname(fileURLToPath(import.meta.url))
for (;;) {
if (basename(directory) !== 'node_modules') {
try {
const manifest = JSON.parse(
readFileSync(join(directory, 'node_modules', name, 'package.json'), 'utf8'),
) as { version?: unknown }
if (typeof manifest.version === 'string') return manifest.version
} catch {
// Not installed at this level; the next one up may have it.
}
}
const parent = dirname(directory)
if (parent === directory) return undefined
directory = parent
}
}
function listTasks(): void {
for (const task of TASKS) {
process.stdout.write(`${task.id}\n ${task.title}\n`)
if (task.needsPeers === true) {
// The one flag a task takes that is not a parameter of its own: the deck
// it compares against, which a shell spells as files.
process.stdout.write(' --against <file> The other maps to compare with; repeat per map\n')
}
for (const param of task.params) {
// A retired question is still taken, as a stored line carries it, and not
// offered: the task it moved to lists it under its own name.
if (param.retired === true) continue
if (paramDerived(param) && param.key === 'balance') {
process.stdout.write(
' --no-balance read the raw counts (balanced by default where the file carries weights)\n',
)
continue
}
const fallback = (param as { default?: unknown }).default
process.stdout.write(
` --${param.key}` +
(fallback === undefined ? '' : ` (default ${JSON.stringify(fallback)})`) +
`${param.label === undefined ? '' : ` ${param.label}`}\n`,
)
}
process.stdout.write('\n')
}
}
/**
* `tasks --json`: the same tasks, as the whole answer rather than a line per flag
* (`analysis/catalogue.ts`) — every value a choice takes, every range, what
* each input reads and what each task writes — for a script or an agent that
* writes commands rather than a person who reads them. Every task the listing
* above names, dev features' included, since the command runs them all; and the
* build on top, as every file the command writes opens with it.
*/
function writeTaskCatalogue(): void {
const catalogue = {
producer: `chromosomix ${VERSION}${COMMIT === '' ? '' : ` (${COMMIT})`}`,
version: VERSION,
// What the four kinds of parameter that name a file take, and what each
// kind of result is written as: the two rules every task shares, said once.
inputs: ENTRY_KINDS,
outputs: OUTPUT_FILES,
tasks: taskCatalogue({ dev: true }),
}
process.stdout.write(`${JSON.stringify(catalogue, null, 2)}\n`)
}
async function runCommand(args: Args, downloads: Downloads): Promise<number> {
const task = taskById(args.command)
if (task === undefined) {
process.stderr.write(`Unknown task ${JSON.stringify(args.command)}. Try \`tasks\`.\n`)
return 2
}
// Parameters and inputs are resolved *before* any file is opened, and a
// failure in either is exit 2 with a sentence rather than a stack: they are
// faults in the command, and a command that is wrong should say so before it
// spends an hour being wrong two hundred times.
let params: Params
let inputs: TaskInputs
let sequences: Map<string, Reference>
let tracks: Map<string, LoadedTrack>
let binning: PairsBinning | undefined
let framing: ReturnType<typeof framingFlags>
try {
params = paramsFor(task, args)
binning = pairsBinningOf(args, task)
framing = framingFlags(args, task)
inputs = bindInputs(task, params, await loadInputs(args, downloads, task))
sequences = await loadSequences(args, downloads, referenceNamed(task, params))
params = withReference(task, params, sequences)
tracks = await loadTrackFiles([{ task, params }], args, downloads)
inputs = withSequenceLabels(withTrackLabels(inputs, tracks), sequences)
// The other maps, reached now where they are addresses: every run mounts
// them, and one that cannot be had is a fault in the command rather than in
// the two hundredth file.
for (const peer of all(args, 'against')) await downloads.reach(peer, true)
} catch (error) {
process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`)
return 2
}
const peers = all(args, 'against')
if (task.needsPeers === true && peers.length === 0) {
// The deck, which a shell has not got: the task's whole question is about
// two files, and a run with one would note "no second map is open" after
// the mount. Said here instead, before anything is opened.
process.stderr.write(
`${task.id} compares this map with another. Name the other with --against <file>.\n`,
)
return 2
}
const directory = one(args, 'out') ?? one(args, 'o') ?? '.'
const quiet = flag(args, 'quiet')
const written = new Set<string>()
if (args.positional.length === 0) {
// No map, which is the 1D browser's own case (§5.8) and only makes sense
// for a task that reads none: a track task over whatever the loaded files
// declare as the assembly. Everything else needs a file to open.
if (task.venue !== 'annotations' || (tracks.size === 0 && sequences.size === 0)) {
process.stderr.write(`${task.id} needs at least one file.\n`)
return 2
}
try {
const result = await runTracksOnly({
task,
params,
inputs,
sequences,
tracks,
peers,
downloads,
...framing,
quiet,
})
for (const note of result.notes) process.stderr.write(` note: ${note}\n`)
await writeOutputs(
result,
stemOf(result.provenance.framing.uri),
directory,
result.contigs,
quiet,
written,
)
return 0
} catch (error) {
process.stderr.write(` failed: ${error instanceof Error ? error.message : String(error)}\n`)
return 1
}
}
const stems = stemsOf(args.positional)
let failures = 0
for (const [index, path] of args.positional.entries()) {
try {
if (!quiet) process.stderr.write(`${displayOf(path)}\n`)
const result = await runOne({
task,
params,
path,
downloads,
binning,
// Not `one(args, 'window')`. `apa` declares a parameter of that name —
// a half-width in bins — and `paramsFor` already gives a task's own
// parameters the flag where the two collide. The framing was reading it
// anyway, so `apa --window 8` set the half-width *and* tried to resolve
// `8` as a locus, and the run died with "Unknown sequence label: 8".
// One name, one meaning, decided by whether the task claims it.
window: task.params.some((param) => param.key === 'window')
? undefined
: one(args, 'window'),
balance: flag(args, 'no-balance') ? false : undefined,
inputs,
sequences,
tracks,
peers,
...framing,
quiet,
})
for (const note of result.notes) process.stderr.write(` note: ${note}\n`)
// Named for the resolution it was measured at where that is the file's
// bins summed (§3.4): beside a run on the file's own rung in one `--out`,
// `sample_1000` and `sample_1000_coarsen4000` are two sets of numbers.
const coarsen = result.provenance.framing.coarsen
const stem = coarsen === undefined ? stems[index] : `${stems[index]}_coarsen${coarsen}`
await writeOutputs(result, stem, directory, result.contigs, quiet, written)
} catch (error) {
failures += 1
// Named and carried on, rather than stopping: a batch of two hundred
// files where the eleventh is truncated should produce a hundred and
// ninety-nine results and one message, not eleven results and a stack.
process.stderr.write(
` failed: ${error instanceof Error ? error.message : String(error)}\n`,
)
} finally {
// A fetched map no later file names again is let go here, so a batch over
// two hundred addresses holds one of them at a time.
if (!namedAgain(args.positional, index)) await downloads.release(path)
}
}
return failures === 0 ? 0 : 1
}
/** Whether a file after `index` names the same file — another resolution of one `.mcool`. */
function namedAgain(paths: readonly string[], index: number): boolean {
// Split by hand rather than by `parseUri`, which refuses an empty file half:
// this runs in a `finally`, and must not throw for a positional that failed.
const fileOf = (path: string): string => path.split('::')[0].trim()
return paths.slice(index + 1).some((later) => fileOf(later) === fileOf(paths[index]))
}
/**
* Re-run a saved tab's analyses over other files.
*
* The parameters come from `analysis` in the tab — the same block the drawer
* restores a form from — so what runs here is what the reader settled on by
* looking at a picture. Nothing is retyped, which is the whole point: a
* transcription error in a batch of two hundred is two hundred wrong numbers
* that look right.
*
* The files are the ones `--over` names and any named after the workspace, so
* `--over data/*.hic` replays every file the shell expands it to. Every one
* after the first was a positional this command never read, and it replayed the
* first alone with exit 0.
*/
async function replayCommand(args: Args, downloads: Downloads): Promise<number> {
const path = args.positional[0]
if (path === undefined) {
process.stderr.write('replay needs a workspace file.\n')
return 2
}
let text: string
try {
text = await readFile((await downloads.local(path, true)) ?? path, 'utf8')
} catch (error) {
process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`)
return 2
}
const read = parseWorkspaceFile(text)
if (isRefusal(read)) {
// The reason rather than one blanket sentence: a workspace from a newer
// build is a different problem from a file that is not one, and only one of
// them is fixed by looking at the file.
process.stderr.write(`${refusalMessage(read, path)}\n`)
return 2
}
// A workspace holds every tab the window had. Replaying "the session" means
// one of them, so it is the tab that was in front unless `--tab` names
// another — printed one-based, because that is how the reader counted them.
const wanted = one(args, 'tab')
const index = wanted === undefined ? read.active : Number(wanted) - 1
if (!Number.isInteger(index) || index < 0 || index >= read.tabs.length) {
process.stderr.write(
`${path} holds ${read.tabs.length} tab${read.tabs.length === 1 ? '' : 's'}; ` +
`--tab must name one of them.\n`,
)
return 2
}
const config = read.tabs[index]
const recorded = recordedTasks(config)
if (recorded.length === 0) {
process.stderr.write(
`${path} records no analysis parameters. Run a task in the app and save again.\n`,
)
return 2
}
// What was recorded is checked as a typed value is (`refusalOf`), before any
// file is opened: a workspace naming an option this build has not got would
// otherwise run the runner's fallback under the recorded name — the false
// provenance a direct run is now refused for.
for (const entry of recorded) {
const task = taskById(entry.task)
for (const spec of task?.params ?? []) {
const refused = refusalOf(spec, entry.params[spec.key])
if (refused === null) continue
process.stderr.write(
`${fileNameOf(path)} recorded ${entry.task} with a value this build cannot run, so ` +
`nothing was replayed. ${refused}\n`,
)
return 2
}
}
const over = [...all(args, 'over'), ...args.positional.slice(1)]
const files = over.length > 0 ? over : [config.state.uri]
const directory = one(args, 'out') ?? one(args, 'o') ?? '.'
const quiet = flag(args, 'quiet')
let sequences: Map<string, Reference>
let tracks: Map<string, LoadedTrack>
let loaded: TaskInputs
let binning: PairsBinning | undefined
let framing: ReturnType<typeof framingFlags>
try {
binning = pairsBinningOf(args)
framing = framingFlags(args)
sequences = await loadSequences(args, downloads)
tracks = await loadTrackFiles(
recorded.flatMap((entry) => {
const task = taskById(entry.task)
return task === undefined ? [] : [{ task, params: entry.params }]
}),
args,
downloads,
config.tracks,
)
loaded = withSequenceLabels(withTrackLabels(await loadInputs(args, downloads), tracks), sequences)
for (const peer of all(args, 'against')) await downloads.reach(peer, true)
} catch (error) {
process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`)
return 2
}
const peers = all(args, 'against')
process.stderr.write(
`${recorded.length} task${recorded.length === 1 ? '' : 's'} from ${fileNameOf(path)}, ` +
`over ${files.length} file${files.length === 1 ? '' : 's'}\n`,
)
const stems = stemsOf(files)
const written = new Set<string>()
let failures = 0
for (const [at, file] of files.entries()) {
// Opened by each task it is replayed under — by range, or from one copy
// fetched whole and let go after the last of them; an address that cannot
// be had fails each of them by name.
for (const entry of recorded) {
const task = taskById(entry.task)
if (task === undefined) {
// A session from a newer build, or one whose task has been withdrawn.
// Named rather than skipped in silence: the count above said how many
// would run and this is why one of them did not.
process.stderr.write(` skipped ${entry.task}: this build has no such task\n`)
continue
}
if (task.needsPeers === true && peers.length === 0) {
// Beside the skip above and for the same reason: the count printed a
// moment ago said how many tasks would run, and a tab that recorded a
// reproducibility run is owed the reason one of them did not. Skipped
// rather than attempted, so it costs no mount and does not turn a
// replay's exit code into a failure over a flag that was not given.
process.stderr.write(
` skipped ${entry.task}: it compares this map with another; name the other with ` +
'--against <file>\n',
)
continue
}
try {
if (!quiet) process.stderr.write(`${displayOf(file)} · ${task.title}\n`)
const result = await runOne({
task,
params: entry.params,
path: file,
downloads,
balance: undefined,
binning,
// Per task, because a replayed workspace can hold several that name
// different sets under different keys.
inputs: bindInputs(task, entry.params, loaded),
sequences,
tracks,
peers,
...framing,
quiet,
})
await writeOutputs(result, stems[at], directory, result.contigs, quiet, written)
} catch (error) {
failures += 1
process.stderr.write(
` failed: ${error instanceof Error ? error.message : String(error)}\n`,
)
}
}
if (!namedAgain(files, at)) await downloads.release(file)
}
return failures === 0 ? 0 : 1
}
/**
* Which sequences of a map join their own ends: the junction test a session
* runs on a map's first open (§8.15), as a table on stdout.
*
* A declaration frames every run after it, so a batch has to make it before the
* first task and hand the same names to each with `--circular` — and a batch
* over eighty genomes, a few of them linear, can neither declare them all round
* nor ask a person which. The same candidates, reads, threshold and balancing
* as the session's (`analysis/circularity.ts`), so what a suite declares is
* what the viewer would have ticked on opening the file at that resolution.
*
* Every sequence gets a row, in the file's order: a score and a verdict where
* the test was run and decided, both empty where it was not — fewer than fifty
* bins at the resolution read, past the fifty longest, or ends that leave fewer
* than two of the three separations to compare: one the balancer dropped, or one
* with nothing on its diagonal. A batch that wants a small plasmid decided reads
* the map at a resolution that gives it fifty bins.
*/
async function circularCommand(args: Args, downloads: Downloads): Promise<number> {
if (args.positional.length === 0) {
process.stderr.write('circular needs at least one file.\n')
return 2
}
const quiet = flag(args, 'quiet')
let binning: PairsBinning | undefined
try {
binning = pairsBinningOf(args)
} catch (error) {
process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`)
return 2
}
let failures = 0
for (const [index, path] of args.positional.entries()) {
try {
downloads.refuseScheme(path)
const { mc } = await openLocal(uriOf(path), { binning, quiet, downloads })
try {
const balance = flag(args, 'no-balance') ? false : mc.hasWeights
const pairs = mc.chromnames.map((name, id) => [name, mc.coords.contigLengths[id]] as const)
// Each where the file puts it, not where `ceil(length / binsize)` would.
const placed = junctionCandidates(pairs, mc.binsize).flatMap((listed) => {
const candidate = placeCandidate(listed, mc.contigExtent(listed.name))
return candidate === null ? [] : [candidate]
})
const measured = await measureJunctions(
placed,
async (rows, cols) => (await mc.matrix({ rows, cols, balance })).values,
)
const lines = [
`# chromosomix ${APP}`,
`# file: ${path}`,
`# test: contacts across each sequence's ends over the diagonal's at ${JUNCTION_BINS} bins ` +
`or fewer, at ${junctionQuorum()} of them at least, on sequences of ` +
`${MIN_JUNCTION_SEQUENCE_BINS} bins or more; circular at ${CIRCULAR_SCORE} or more (§8.15)`,
`# framing: ${mc.binsize} bp${balance ? ', balanced' : ''}`,
['sequence', 'length', 'score', 'circular'].join('\t'),
]
for (const [name, length] of pairs) {
const score = measured?.scores[name]
lines.push(
[
name,
String(length),
score === undefined ? '' : score.toFixed(4),
score === undefined ? '' : score >= CIRCULAR_SCORE ? 'yes' : 'no',
].join('\t'),
)
}
process.stdout.write(`${lines.join('\n')}\n`)
} finally {
mc.close()
}
} catch (error) {
failures += 1
process.stderr.write(` failed: ${error instanceof Error ? error.message : String(error)}\n`)
} finally {
if (!namedAgain(args.positional, index)) await downloads.release(path)
}
}
return failures === 0 ? 0 : 1
}
/**
* `pairtools stats` for each `.pairs` named, as the app's import counts it (§3.7).
*
* The counts are the import's own (`pairs/stats.ts`), made by the import's own
* pass — binned at one bin a sequence, which costs nothing, so that what this
* writes and what the General column shows of the same file are one count. A
* file with no `#chromsize:` is refused as the import refuses it: the sizes are
* the last section of the file, and the bin table the pass is built on.
*
* The one file this command writes with no `#` lines over it. pairtools reads a
* `.stats` back a `key<TAB>value` a line and refuses any other, and the point
* of writing its format is that it is read by what reads pairtools' — MultiQC,
* `pairtools stats --merge`. Where it came from is said on stderr instead.
*/
async function statsCommand(args: Args, downloads: Downloads): Promise<number> {
if (args.positional.length === 0) {
process.stderr.write('stats needs at least one .pairs file.\n')
return 2
}
const directory = one(args, 'out') ?? one(args, 'o')
const quiet = flag(args, 'quiet')
const stems = stemsOf(args.positional)
let failures = 0
for (const [index, path] of args.positional.entries()) {
let source: ByteSource | null = null
try {
if (!quiet) process.stderr.write(`${displayOf(path)}\n`)
downloads.refuseScheme(path)
const where = await downloads.where(uriOf(path), false)
source = where.kind === 'range' ? where.source : await LocalFileSource.fromPath(where.path)
await source.mount()
if (!(await isPairsFile(source))) {
throw new Error(`${fileNameOf(path)} is not a .pairs file: it does not begin with a \`## pairs format\` line.`)
}
const header = await readPairsHeader(source)
const widest = header.contigs.reduce((most, contig) => Math.max(most, contig.length), 1)
let shown = -1
const binned = await binPairs(source, {
binSize: widest,
contigs: header.contigs,
columns: header.columns,
...(quiet
? {}
: {
onProgress: (done: number, total: number) => {
const percent = total > 0 ? Math.floor((done / total) * 100) : 0
if (percent === shown) return
shown = percent
process.stderr.write(`\r counting records: ${percent}% `)
},
}),
})
if (!quiet) process.stderr.write('\r')
if (binned?.stats == null) throw new Error('the count was interrupted')
const text = writePairtoolsStats(binned.stats)
if (directory === undefined) {
process.stdout.write(text)
} else {
await mkdir(directory, { recursive: true })
const at = join(directory, `${stems[index]}.stats`)
await writeFile(at, text)
if (!quiet) process.stderr.write(` wrote ${at}\n`)
}
if (!quiet) process.stderr.write(` ${statsLine(binned.stats)}\n`)
} catch (error) {
failures += 1
process.stderr.write(` failed: ${error instanceof Error ? error.message : String(error)}\n`)
} finally {
source?.close()
if (!namedAgain(args.positional, index)) await downloads.release(path)
}
}
return failures === 0 ? 0 : 1
}
/** The few numbers a reader looks at first, on one line of stderr. */
function statsLine(stats: PairStats): string {
const pct = (part: number, whole: number): string => (whole > 0 ? `${((100 * part) / whole).toFixed(1)}%` : '—')
return (
`${stats.total.toLocaleString('en-US')} records · ${pct(stats.totalMapped, stats.total)} mapped · ` +
`${pct(stats.totalDups, stats.totalMapped)} duplicates · ${pct(stats.cis, stats.totalNodups)} cis`
)
}
/**
* Boost-HiC's map of each sequence, as an oversample makes it (§6.5) and as
* Boost-HiC's own `main.py` writes it.
*
* An oversample draws a sequence's new contacts from that map, and nothing else
* shows it: what reaches the screen is a draw from it, and a draw is a poor way
* to hold a port to its upstream. So this hands Boost-HiC the square an
* oversample hands it — the sequence's stored counts through `cisSquare` and
* `boostSteps` — and writes what `main.py` writes, `boostedmat`: the boosted
* map over the bins its outlier filter kept, in SCN units: the map to hold the
* port to Boost-HiC's Python by, cell for cell over whole chromosomes, where the
* golden holds a hundred bins.
*
* One square per sequence, rows and columns named by each kept bin's start;
* the bins the filter took out are the ones not named. A sequence past
* {@link BOOST_MAX_BINS} is refused by name, as an oversample refuses it, and
* the others are still written.
*/
async function boostCommand(args: Args, downloads: Downloads): Promise<number> {
if (args.positional.length === 0) {
process.stderr.write('boost needs at least one file.\n')
return 2
}
const asked = one(args, 'alpha')
const alpha = asked === undefined ? BOOST_ALPHA : Number(asked)
if (!Number.isFinite(alpha) || alpha <= 0) {
process.stderr.write(`--alpha needs a positive number; got ${JSON.stringify(asked)}.\n`)
return 2
}
const named = all(args, 'sequences').flatMap((item) => item.split(',')).filter((item) => item !== '')
const directory = one(args, 'out') ?? one(args, 'o') ?? '.'
const quiet = flag(args, 'quiet')
let failures = 0
for (const [index, path] of args.positional.entries()) {
try {
if (!quiet) process.stderr.write(`${path}\n`)
downloads.refuseScheme(path)
const { mc } = await openLocal(uriOf(path), { binning: pairsBinningOf(args), quiet, downloads })
try {
// The two maps an oversample refuses, for the reasons it gives (§6.5):
// a sum of cells is not one library, and a square store holds every
// contact twice, which the square below would then count twice.
if (mc.cells.length > 0) {
throw new Error('a single-cell container’s map is a sum of its cells rather than one library.')
}
if (mc.storageMode !== 'symmetric-upper') {
throw new Error('this map stores both triangles, and a boost reads an upper-triangular one.')
}
for (const name of named.length === 0 ? mc.chromnames : named) {
const id = mc.chromnames.indexOf(name)
if (id < 0) {
failures += 1
process.stderr.write(` failed: ${fileNameOf(path)} has no sequence ${name}.\n`)
continue
}
const [from, to] = mc.contigExtent(id)
const n = to - from
if (n > BOOST_MAX_BINS) {
failures += 1
process.stderr.write(
` failed: ${name} is ${n.toLocaleString('en-US')} bins at this resolution, and a boost ` +
`walks every path between them: at most ${BOOST_MAX_BINS.toLocaleString('en-US')}. ` +
'Open a coarser resolution.\n',
)
continue
}
const started = Date.now()
const steps = boostSteps(cisSquare(await cisPixels(mc, from, to), from, n), n, alpha)
if (steps === null) {
process.stderr.write(` note: ${name}: fewer than two bins survive the outlier filter.\n`)
continue
}
const lines = [
`# chromosomix ${APP}`,
`# created: ${new Date().toISOString()}`,
`# file: ${path}`,
'# method: Boost-HiC (Carron et al. 2019): the outlier filter, SCN, shortest paths on ' +
'1/SCN^alpha, adjusted to P(s) (§6.5)',
`# alpha: ${alpha}`,
`# sequence: ${name}, ${n} bins at ${mc.binsize} bp, ${steps.kept.length} kept`,
'# units: SCN',
]
const starts = Array.from(steps.kept, (bin) => String(bin * mc.binsize))
lines.push(['start', ...starts].join('\t'))
const size = steps.kept.length
for (let row = 0; row < size; row++) {
const cells = [starts[row]]
for (let col = 0; col < size; col++) {
cells.push(String(Number(steps.boosted[row * size + col].toPrecision(10))))
}
lines.push(cells.join('\t'))
}
await mkdir(directory, { recursive: true })
const file = join(directory, `${stemOf(path)}.boost-${name.replace(/[\\/\s]+/g, '_')}.tsv`)
await writeFile(file, `${lines.join('\n')}\n`)
if (!quiet) {
process.stderr.write(
` ${name}: ${steps.kept.length} of ${n} bins kept, ${((Date.now() - started) / 1000).toFixed(1)} s; ` +
`wrote ${file}\n`,
)
}
}
} finally {
mc.close()
}
} catch (error) {
failures += 1
process.stderr.write(` failed: ${error instanceof Error ? error.message : String(error)}\n`)
} finally {
if (!namedAgain(args.positional, index)) await downloads.release(path)
}
}
return failures === 0 ? 0 : 1
}
/**
* The stored pixels of one sequence's own block, as an oversample collects them
* before it draws: every row of the sequence read as a band, kept where the
* column is in it too, an empty pixel skipped.
*/
async function cisPixels(
mc: MetaCooler,
from: number,
to: number,
): Promise<{ bin1: Int32Array; bin2: Int32Array; count: Float64Array }> {
const bin1: number[] = []
const bin2: number[] = []
const count: number[] = []
await mc.storedPixels.forEachBands([[from, to]], (chunk) => {
for (let i = 0; i < chunk.length; i++) {
if (chunk.count[i] === 0 || chunk.bin2[i] < from || chunk.bin2[i] >= to) continue
bin1.push(chunk.bin1[i])
bin2.push(chunk.bin2[i])
count.push(chunk.count[i])
}
})
return { bin1: Int32Array.from(bin1), bin2: Int32Array.from(bin2), count: Float64Array.from(count) }
}
/** The tasks a session recorded parameters for, in catalogue order. */
export function recordedTasks(config: {
analysis?: Record<string, Params> | undefined
}): Array<{ task: string; params: Params }> {
const held = config.analysis
if (held === undefined || held === null) return []
const out: Array<{ task: string; params: Params }> = []
for (const task of TASKS) {
const params = held[task.id]
if (params !== undefined) out.push({ task: task.id, params })
}
// A task this build does not know is still reported, so `replay` can say so
// rather than quietly running fewer than it announced.
for (const [id, params] of Object.entries(held)) {
if (!out.some((entry) => entry.task === id)) out.push({ task: id, params })
}
return out
}
/** `demo/yeast/Yeast_microC.cool` → `Yeast_microC`. */
export function stemOf(path: string): string {
// The `::` half is the *group inside the container*, so a file addressed as
// `sample.mcool::/resolutions/1000` is still `sample` — it was `1000`, which
// is `basename` of a group path and named every output after a number. The
// group's last segment is kept as a suffix so two resolutions of one file
// written to one `--out` are two sets of results rather than one overwritten
// twice.
const { path: file, group } = uriParts(path)
const name = fileNameOf(file)
const dot = name.indexOf('.')
const stem = dot > 0 ? name.slice(0, dot) : (name || 'output')
return `${stem}${groupSuffix(group)}`
}
/**
* `parseUri`, without its refusal of an empty file half: the stems of a batch
* are named before its first run, and a positional the run would refuse is
* refused there, as that file's failure, rather than here as the batch's.
*/
function uriParts(path: string): { path: string; group: string } {
try {
return parseUri(path)
} catch {
return { path: '', group: '/' }
}
}
/** `_1000` for `::/resolutions/1000`, and nothing for a file's root. */
function groupSuffix(group: string): string {
if (group === '/') return ''
const last = group.split('/').filter((part) => part !== '').pop()
return last === undefined ? '' : `_${last}`
}
/**
* One stem per input of a command, no two alike: the names its outputs are
* written under.
*
* {@link stemOf} of each wherever that is unique, so a command over one file —
* or over files that differ before their first dot — names its outputs as it
* always has, and a script reading them back keeps working. It was the only
* rule, so `coverage HCT116.rep1.cool HCT116.rep2.cool` wrote
* `HCT116.coverage.*` twice, the second run's files over the first's, with exit
* 0; and `dirA/sample.mcool dirB/sample.mcool` did the same. Where two would
* share a stem, those two keep more of their names, a step at a time, until
* they differ:
*
* 1. the whole name less its format extension, and a `.gz` before it:
* `HCT116.rep1` and `HCT116.rep2`;
* 2. the whole name: `sample.cool` and `sample.hic`;
* 3. the directories it is in, nearest first, joined with `_` — an address's
* path, then its host: `dirA_sample` and `dirB_sample`;
* 4. and a file named twice is numbered in the order given: `sample`,
* `sample_2`.
*
* Compared without case, because two names that differ only in it are one file
* on a Mac's disk and on Windows'.
*/
export function stemsOf(paths: readonly string[]): string[] {
const ladders = paths.map(stemLadder)
// What each input *is*: one file named twice, or two names differing only in
// case, can never be told apart by more of its name, and climbing for it
// would only end at a stem made of every directory up to the root.
const identity = paths.map((path) => {
const { path: file, group } = uriParts(path)
return `${isAddress(file) ? file : resolve(file)}::${group}`.toLowerCase()
})
const rung = paths.map(() => 0)
const stems = ladders.map((ladder) => ladder[0])
for (;;) {
const holders = new Map<string, number[]>()
stems.forEach((stem, index) => {
const key = stem.toLowerCase()
holders.set(key, [...(holders.get(key) ?? []), index])
})
const climbing = [...holders.values()].flatMap((held) =>
held.filter(
(index) =>
rung[index] < ladders[index].length - 1 &&
held.some((other) => identity[other] !== identity[index]),
),
)
if (climbing.length === 0) break
for (const index of climbing) {
rung[index] += 1
stems[index] = ladders[index][rung[index]]
}
}
const taken = new Set<string>()
return stems.map((stem) => {
let named = stem
for (let count = 2; taken.has(named.toLowerCase()); count++) named = `${stem}_${count}`
taken.add(named.toLowerCase())
return named
})
}
/** Every stem {@link stemsOf} may give one input, least specific first. */
function stemLadder(path: string): string[] {
const { path: file, group } = uriParts(path)
const name = fileNameOf(file)
const suffix = groupSuffix(group)
const bare = name.replace(/\.(gz|bgz|bz2|xz|zst)$/i, '')
const dot = bare.lastIndexOf('.')
const long = `${dot > 0 ? bare.slice(0, dot) : bare || name || 'output'}${suffix}`
const ladder = [stemOf(path), long, `${name || 'output'}${suffix}`]
const directories = isAddress(file)
? addressDirectories(file)
: resolve(file)
.split(/[\\/]/)
.filter((part) => part !== '')
.slice(0, -1)
.reverse()
let prefix = ''
for (const directory of directories) {
// `:` and the separators are no part of a file's name: a drive on Windows,
// the port of an address's host, a `%2F` an address decoded to.
const safe = directory.replace(/[:\\/]/g, '_')
prefix = prefix === '' ? safe : `${safe}_${prefix}`
ladder.push(`${prefix}_${long}`)
}
return ladder.filter((stem, at) => ladder.indexOf(stem) === at)
}
export async function main(argv: readonly string[]): Promise<number> {
// Asked for anywhere, the help, before the rest is checked: a reader who
// types `--help` after half a command wants the usage, not a refusal of the half.
if (argv.includes('--help')) {
process.stdout.write(USAGE)
return 0
}
// The version on the same terms — after the help, which is the longer answer
// to a line that asks for both.
if (argv.includes('--version')) {
process.stdout.write(versionText())
return 0
}
let args: Args
try {
const command = commandOf(argv)
if (command === '' || command === 'help') {
process.stdout.write(USAGE)
return 0
}
if (command === 'tasks') {
if (argv.includes('--json')) writeTaskCatalogue()
else listTasks()
return 0
}
if (!['replay', 'circular', 'boost', 'stats'].includes(command) && taskById(command) === undefined) {
process.stderr.write(`Unknown task ${JSON.stringify(command)}. Try \`tasks\`.\n`)
return 2
}
args = parseArgs(argv, command)
} catch (error) {
if (!(error instanceof UsageError)) throw error
process.stderr.write(`${error.message}\n`)
return 2
}
if (flag(args, 'help')) {
process.stdout.write(USAGE)
return 0
}
if (args.flags.has('balance') && !takesBalance(args.command)) {
process.stderr.write(
'--balance is the default now: a map is read balanced wherever the file carries weights. ' +
'Drop it, or use --no-balance for the raw counts.\n',
)
return 2
}
const threads = one(args, 'threads')
const count = threads === undefined ? DEFAULT_THREADS : Number(threads)
if (!Number.isInteger(count) || count < 1) {
process.stderr.write(`--threads ${threads}: a whole number of threads, 1 or more.\n`)
return 2
}
useThreads(count)
// One directory of fetched addresses per command, gone when it ends — after
// a failure as after a success, which is what the `finally` is for.
const downloads = new Downloads({ quiet: flag(args, 'quiet') })
try {
if (args.command === 'replay') return await replayCommand(args, downloads)
if (args.command === 'circular') return await circularCommand(args, downloads)
if (args.command === 'boost') return await boostCommand(args, downloads)
if (args.command === 'stats') return await statsCommand(args, downloads)
return await runCommand(args, downloads)
} finally {
await downloads.close()
}
}
// `import.meta.url` against `process.argv[1]` is the ESM spelling of "am I the
// entry point"; importing this module from a test must not run it. Compared
// by realpath rather than by name: Node resolves the entry file's own symlinks
// before it becomes `import.meta.url`, so an extensionless `bin` link — the
// whole point of `package.json`'s `bin` field — has `argv[1]` end in
// `chromosomix` while the module it loaded ends in `chromosomix.mjs`.
// A name or suffix comparison never matches there; realpath resolves both
// sides to the same file underneath the symlink.
function isEntryPoint(argv1: string | undefined): boolean {
if (argv1 === undefined) return false
try {
return import.meta.url === pathToFileURL(realpathSync(argv1)).href
} catch {
// Not a path Node can stat — cannot be the file that is executing.
return false
}
}
/**
* Let a reader stop reading.
*
* `chromosomix tasks | head -1`, or a `less` quit before the end: the other end
* of the pipe closes, and Node reports the next write as an error on the stream
* — `EPIPE`, or `EOF` on Windows — which unheard is an uncaught exception, so
* the command died with a stack trace and exit 1 the moment `head` had its
* line. Heard, what was left to print is dropped, and the command finishes what
* it was doing and exits with the status it would have had. Not with a
* `process.exit()` on the spot: a task's progress and notes go to stderr, so
* `insulation map.cool 2>&1 | head -1` would have stopped with its files half
* written under an exit code that said nothing was wrong. Any other error on
* the stream is thrown, as it was.
*/
export function ignoreClosedPipe(stream: NodeJS.WritableStream): void {
stream.on('error', (error: NodeJS.ErrnoException) => {
if (error.code === 'EPIPE' || error.code === 'EOF') return
throw error
})
}
// A helper thread runs this same file (`cli/threads.ts`), and has the same
// `argv[1]`: it serves the thread that started it, and is no command at all.
const invoked = !serveIfHelper() && isMainThread && isEntryPoint(process.argv[1])
if (invoked) {
ignoreClosedPipe(process.stdout)
ignoreClosedPipe(process.stderr)
main(process.argv.slice(2))
.then((code) => {
process.exitCode = code
})
.catch((error: unknown) => {
process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`)
process.exitCode = 1
})
}
|