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* Everything the file says about one alignment, on being asked.
*
* {@link openFeatureDialog}'s sibling, and deliberately its twin in shape: a
* click on a read opens a card that stays open, holds what the record actually
* carried, and can be selected and copied out of. A read is a worse tooltip
* subject than a gene and a better card subject — the facts a reader wants are
* its flags, its CIGAR and where its mate went, and none of the three fits in
* two lines following a pointer.
*
* What it does *not* do is fetch. Every field here is already in the
* {@link ReadPile} the lane drew, which is the reason a click can answer
* instantly and the reason the answer cannot disagree with the picture: the
* card and the rectangle are made of the same numbers.
*
* Browser-only, like the pile it comes from (§8.13). There is no read to click
* beside a heatmap, because there is no read drawn there.
*/
import { formatLocus, formatPosition } from '../genome/assembly'
import { CIGAR_OPS, FLAG } from '../annotations/bam/format'
import type { ReadPile } from '../annotations/types'
import { modLabel } from '../annotations/bam/basemods'
import { Modal } from './Modal'
import { el, fmt } from './dom'
import { icon } from './icons'
export interface ReadDialogProps {
pile: ReadPile
index: number
/** What the lane it came from is called, for the line that says where. */
source: string
/** Frame the view on this read, and close. */
onGoTo?(): void
onClose?(): void
}
/** One `key: value` line. The value is selectable; that is half the point. */
function row(key: string, value: string): HTMLElement {
return el(
'div',
{ class: 'feature-row' },
el('span', { class: 'feature-key', text: key }),
el('span', { class: 'feature-val', text: value }),
)
}
/**
* The SAM flag in words.
*
* Every bit that is set, named the way the specification names it, plus the raw
* number in brackets — because the number is what a reader will paste into
* `samtools view -f`, and a card that hid it would be a card they had to work
* around. Bits nobody set are simply absent: listing twelve rows of "no" to
* carry two of "yes" is how a card stops being read.
*/
const FLAG_WORDS: Array<[number, string]> = [
[FLAG.PAIRED, 'paired'],
[FLAG.PROPER_PAIR, 'proper pair'],
[FLAG.UNMAPPED, 'unmapped'],
[FLAG.MATE_UNMAPPED, 'mate unmapped'],
[FLAG.REVERSE, 'reverse'],
[FLAG.MATE_REVERSE, 'mate reverse'],
[FLAG.FIRST_IN_PAIR, 'first in pair'],
[FLAG.SECOND_IN_PAIR, 'second in pair'],
[FLAG.SECONDARY, 'secondary'],
[FLAG.QC_FAIL, 'QC fail'],
[FLAG.DUPLICATE, 'duplicate'],
[FLAG.SUPPLEMENTARY, 'supplementary'],
]
function flagText(flags: number): string {
const set = FLAG_WORDS.filter(([bit]) => (flags & bit) !== 0).map(([, word]) => word)
return set.length === 0 ? `none (${flags})` : `${set.join(', ')} (${flags})`
}
/**
* The CIGAR, rebuilt from the ops the pile is holding.
*
* Long ones are cut, because a spliced long read can carry hundreds of
* operations and a card is not a place to scroll through them. What is kept is
* the head, which is where the clipping and the first blocks are — the part
* anyone reads a CIGAR for.
*/
const CIGAR_LIMIT = 24
function cigarText(pile: ReadPile, at: number): string {
const from = pile.opAt[at]
const to = pile.opAt[at + 1]
const n = to - from
if (n <= 0) return '—'
const shown = Math.min(n, CIGAR_LIMIT)
let out = ''
for (let i = from; i < from + shown; i++) {
out += `${pile.opLen[i]}${CIGAR_OPS[pile.opCode[i]] ?? '?'}`
}
return shown < n ? `${out}… (${n} operations)` : out
}
/**
* Where the mate is, in one line.
*
* Three genuinely different answers and they are worth distinguishing: on the
* same sequence (the ordinary case, and then the insert size means something),
* on another one (a translocation, a scaffolding artefact, or a viral
* integration — the reason anyone colours by mate at all), and nowhere.
*/
function mateText(pile: ReadPile, at: number): string {
if ((pile.flags[at] & FLAG.PAIRED) === 0) return 'unpaired'
if ((pile.flags[at] & FLAG.MATE_UNMAPPED) !== 0) return 'unmapped'
const contig = pile.mateContig[at]
const position = pile.matePos[at]
if (contig < 0 || position < 0) return 'not recorded'
const name = pile.contigs[contig] ?? '?'
const where = formatPosition(name, position)
const strand = (pile.flags[at] & FLAG.MATE_REVERSE) !== 0 ? 'reverse' : 'forward'
return name === pile.contig ? `${where} (${strand})` : `${where} (${strand}, other sequence)`
}
/** How many bases of this read disagree with the reference, where any do. */
function diffCount(pile: ReadPile, at: number): number {
return pile.diffAt[at + 1] - pile.diffAt[at]
}
/** `5mC (m) 41 calls, 30 modified · 5hmC (h) 41 calls, 2 modified`, or `''`. */
function modSummary(pile: ReadPile, at: number): string {
const mods = pile.mods
if (mods === undefined) return ''
const calls = new Map<number, [number, number]>()
for (let k = mods.at[at]; k < mods.at[at + 1]; k++) {
const held = calls.get(mods.code[k]) ?? [0, 0]
held[0]++
if (mods.prob[k] >= 128) held[1]++
calls.set(mods.code[k], held)
}
if (calls.size === 0) return 'none in its MM/ML tags'
return [...calls.entries()]
.sort((a, b) => a[0] - b[0])
.map(([code, [n, modified]]) => `${modLabel(mods.codes[code] ?? '')} ${fmt.int(n)} calls, ${fmt.int(modified)} modified`)
.join(' · ')
}
/** Open the card. Returns the modal so the caller can hold and dismiss it. */
export function openReadDialog(props: ReadDialogProps): Modal {
const { pile, index: at } = props
const name = pile.names[at] ?? ''
const start = pile.refStart[at]
const end = pile.refEnd[at]
const flags = pile.flags[at]
return new Modal({
// The name, when the pile kept one. It only does at the zoom where reads are
// wide enough for a reader to have been aiming at a particular one, which is
// also the only zoom at which one can be clicked — so in practice this is
// always the name, and the fallback is a guard rather than a case.
title: name === '' ? 'Read' : name,
...(props.onClose === undefined ? {} : { onClose: props.onClose }),
body: (close) => {
const rows: HTMLElement[] = [
// The name again, under the title, and this is not a duplicate for its
// own sake: the heading is uppercased by the house style and a read name
// is a case-sensitive identifier somebody is going to paste into
// `samtools view | grep`. Here it is selectable and exactly as the file
// wrote it. `FeatureDialog` repeats a gene's name for the same reason.
...(name === '' ? [] : [row('name', name)]),
row('position', formatLocus({ contig: pile.contig, start, end })),
// The *aligned* span, and the label says so: a spliced read covers ten
// kilobases and is a hundred bases long, and "length" alone would be the
// card asserting the wrong one of those.
row('aligned span', fmt.bp(end - start)),
row('strand', (flags & FLAG.REVERSE) !== 0 ? 'reverse (−)' : 'forward (+)'),
row('mapping quality', pile.mapq[at] === 255 ? 'not available (255)' : String(pile.mapq[at])),
row('flags', flagText(flags)),
row('CIGAR', cigarText(pile, at)),
]
const clipped = pile.clipStart[at] + pile.clipEnd[at]
if (clipped > 0) {
rows.push(row('soft clipped', `${pile.clipStart[at]} before, ${pile.clipEnd[at]} after`))
}
rows.push(row('mate', mateText(pile, at)))
// Only where the file wrote one. `0` is what an unpaired or
// single-ended record carries, and printing "insert size: 0" would be
// reporting a measurement nobody made.
if (pile.tlen[at] !== 0) {
rows.push(row('insert size', `${fmt.int(Math.abs(pile.tlen[at]))} bp`))
}
const diffs = diffCount(pile, at)
if (diffs > 0) rows.push(row('mismatches', String(diffs)))
// The read's modification calls, by code, where the pile carries them
// (§8.13): how many bases each was called on and how many of those
// cleared one half — the threshold-free count, since the card is about
// the record and the lane's threshold is a reading of it.
const mods = modSummary(pile, at)
if (mods !== '') rows.push(row('modifications', mods))
// Which category this read was coloured as. Worth a row: the colouring is
// a control the reader set, and a card that showed the read without
// saying which bucket it landed in leaves the legend to be read backwards
// off the picture.
const group = pile.groups[pile.group[at]]
if (group !== undefined && pile.groups.length > 1) rows.push(row('group', group))
rows.push(row('track', props.source))
const foot = el('div', { class: 'feature-foot' })
if (props.onGoTo !== undefined) {
const go = props.onGoTo
const button = el('button', {
class: 'btn btn-keyed',
type: 'button',
title: 'Frame the view on this read, with a little room either side',
})
button.append(icon('zoom-in', { size: 14 }), el('span', { text: 'zoom to it' }))
button.addEventListener('click', () => {
close()
go()
})
foot.append(button)
}
return el('div', { class: 'feature-body' }, el('div', { class: 'feature-rows' }, ...rows), foot)
},
})
}
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