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* The map report, as a descriptor.
*
* One run that answers the questions a library is judged by before anything is
* read off it — how many contacts, how many cis, how they decay, how evenly they
* cover the genome, which sequences keep to themselves, and down to which bin
* size the map still has contacts in most of its bins — and one page that holds
* the answers, written from the run (`analysis/report/page.ts`).
*
* **A composite** (§18.2): P(s), coverage and cis and trans per sequence are
* those tasks' own runs, at their own defaults but for what is answered here
* ({@link upstreamParams}), so the numbers in the report are the numbers each
* task gives on its own, and a run of any of them already in hand is reused.
* What it adds is the library's totals and the resolution ladder
* (`analysis/mapreport.ts`).
*
* **Numbers only.** Nothing in the report passes or fails: Rao et al.'s map
* resolution and every other cut in the field is a threshold somebody chose,
* and the report gives what a cut is applied to instead (§18.9's argument,
* applied to a verdict as it is to a call).
*/
import { mapReportPage } from '../report/page'
import { multiqcLadder, multiqcPs, multiqcResolution, multiqcSummary } from '../report/multiqc'
import type { AnalysisContext, AnalysisTask, CostEstimate, ParamSpec, Params } from '../types'
import { NEEDS_MAP, READY, waitingFor } from '../types'
import { BALANCE_PARAM } from './shared'
const PARAMS: readonly ParamSpec[] = [
{
kind: 'choice',
key: 'base',
label: 'ladder from',
hint: 'The resolution the library is counted at and the ladder climbs from.',
default: 'finest',
options: [
{
value: 'finest',
label: 'the file’s finest resolution',
hint: 'Where the file stores more than one, its finest is read for the ladder, whatever is on screen.',
},
{ value: 'map', label: 'this map’s resolution' },
],
},
// P(s) is read balanced where the file is, as the P(s) task reads it; the
// coverage and the cis and trans are always the raw counts, since a balanced
// coverage is flat by construction and says nothing about depth.
BALANCE_PARAM,
]
function estimate(context: AnalysisContext, params: Params): CostEstimate {
const finest =
params.base !== 'map' && context.resolutions !== undefined && context.resolutions.length > 0
? Math.min(...context.resolutions)
: context.binsize
const at = finest < context.binsize ? `the file’s finest resolution, ${finest.toLocaleString()} bp` : 'this map'
return {
class: 'scan',
requests: null,
bytes: null,
note: `One pass over the pixel table of ${at}, beside the runs of P(s), coverage and cis and trans`,
}
}
export const MAP_REPORT_TASK: AnalysisTask = {
id: 'mapreport',
title: 'Map report',
blurb: 'A library’s QC on one page: its contacts, their decay and coverage, and the resolutions it can bear.',
keywords: ['QC', 'quality', 'report', 'map resolution', 'MultiQC', 'summary', 'depth'],
group: '2d',
venue: 'analysis',
version: 1,
availability: (context) => (context.hasMap ? READY : waitingFor(NEEDS_MAP)),
params: PARAMS,
outputs: ['table', 'curve'],
requires: ['expected', 'coverage', 'cistrans'],
upstreamParams: (id, params): Params => {
if (id === 'expected') return { scope: 'file', balance: params.balance === true }
if (id === 'coverage') return { total: true, fraction: false, cis: false, trans: false, balance: false }
// Cis and trans of the counts, as the library's own totals are: a share of
// balanced values is a share of something no read measured.
if (id === 'cistrans') return { balance: false }
return {}
},
documents: [
{ id: 'report', extension: 'html', label: 'HTML report', type: 'text/html', write: mapReportPage },
{ id: 'summary_mqc', extension: 'tsv', label: 'MultiQC summary', type: 'text/tab-separated-values', shellOnly: true, write: multiqcSummary },
{ id: 'resolutions_mqc', extension: 'tsv', label: 'MultiQC resolutions', type: 'text/tab-separated-values', shellOnly: true, write: multiqcLadder },
{ id: 'resolution_mqc', extension: 'json', label: 'MultiQC contacts per bin', type: 'application/json', shellOnly: true, write: multiqcResolution },
{ id: 'ps_mqc', extension: 'json', label: 'MultiQC P(s)', type: 'application/json', shellOnly: true, write: multiqcPs },
],
estimate,
}
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