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42x 42x 42x 42x 42x 42x 42x 42x 42x 42x 42x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 3x 2x 2x 2x 2x 2x 14x 14x 2x 40x 40x 40x 40x 40x 40x 2x 83x 83x 20x 20x 20x 2x 2x 4x 4x 12x 4x 4x 2x | /**
* Drawing a pile of reads, and the pairs between them.
*
* ## Where a pile can be drawn at all
*
* A BAM imports as two rows (§8.13): its depth, which is a coverage profile
* `drawTrack` paints like any other track, and the pile — this module. So there
* is no rung here at which this lane draws a curve. There are only the two at
* which it draws anything:
*
* - **reads**, individual molecules in packed rows, once a read is wider than a
* few pixels;
* - **bases**, the same pile with a letter in every column, once a base owns
* one.
*
* …and `none` for everywhere else, where the lane says *zoom in* rather than
* drawing a smear. {@link readRungFor} is the whole of that decision and it
* takes the *surface* as an argument. Beside a heatmap the axis is an axis of
* matrix bins, where the finest unit is a bin rather than a base — so there is
* nothing for a read to be drawn on, and the answer there is always `none`. The
* rule is geometry rather than policy, but it is stated as a rule because the
* geometry alone cannot enforce it: `basePixels` measures pixels per *axis
* unit*, and a map zoomed into a fine cooler has the same pixels-per-unit as a
* browser.
*
* ## Why the pile is not just rectangles
*
* A read is a rectangle only when nothing happened to it. What a reader is
* looking for is the exceptions, and each is a different mark: an insertion is
* a tick *between* two bases and has no width of its own; a deletion is a gap
* with a line through it, because the read spans it and asserts it is not
* there; a spliced gap is a thin line with no ink, because the read says
* nothing about what it skipped; and a soft clip is drawn faintly outside the
* aligned extent, because a read that is half clipped is telling you something
* about the alignment rather than about the genome.
*/
import { BASE_COLOURS } from './sequence'
/**
* The glyph for a `BASE_CODE` value.
*
* `BASE_CODE` maps every one of 256 bytes into `0..4`, so this is total — and
* it is the inverse of that table rather than a second opinion about it, which
* is why it is five entries in the same order as {@link BASE_COLOURS}.
*/
const BASE_LETTERS = ['A', 'C', 'G', 'T', 'N'] as const
import {
canvasToAcross,
laneBands,
laneIsHorizontal,
laneRect,
laneX,
laneY,
type LaneFrame,
} from './lane'
import { basePixels } from './sequence'
import { rotateHue } from './hue'
import type { PairLayout, ReadPile } from '../annotations/types'
import { FLAG } from '../annotations/bam/format'
import { modStateOf, probabilityOf } from '../annotations/bam/basemods'
/** The one flag bit this module draws differently; see {@link drawOne}. */
const SUPPLEMENTARY = FLAG.SUPPLEMENTARY
import { stretchOf, unitAt, type LocusAxis, type LocusSegment } from './locus'
/**
* Which picture a pile lane draws, if any.
*
* `none` is the answer everywhere a read is narrower than the ink it would take
* — the lane says *zoom in* rather than drawing a smear. It used to be called
* `coverage`, because the depth curve shared the lane and was what a reader saw
* out here; the depth is a row of its own now (§8.13) and this rung draws
* nothing at all.
*/
export type ReadRung = 'none' | 'reads' | 'bases'
/** Which surface is asking — the one thing geometry cannot answer for itself. */
export type LaneSurface = 'browser' | 'map'
/** A read narrower than this is thinner than the ink it would be drawn with. */
const READ_MIN_PIXELS = 2.5
/** …and below this many pixels per base, a letter does not fit in a column. */
const LETTER_MIN_PIXELS = 7
/**
* The stretch of the axis a pile was fetched for.
*
* The first stretch of its contig on most axes; on an edited one (§27.2) a
* contig can be several pieces, and a pile belongs to the one whose piece its
* window overlaps — a window is cut per piece, so there is exactly one.
*/
function pileSegment(axis: LocusAxis, pile: ReadPile): LocusSegment | null {
for (const segment of axis.segmentsOf(pile.contig)) {
if (!(segment.bpPerUnit > 0)) continue
const [from, to] = stretchOf(segment)
if (pile.end > from && pile.start < to) return segment
}
return null
}
/**
* Which rung this frame is on.
*
* `surface` is not advisory. A pile exists only in the 1D browser (§8.13), and
* this is the one place that is decided — so a caller on the map gets `none`
* whatever its zoom, and cannot get anything else by arriving with a frame that
* happens to be finely scaled.
*
* `bpPerUnit` converts the frame's own units into base pairs. It is `1` in the
* browser, where the axis is the assembly laid out at one unit per base, and it
* is the bin size beside a map — which is exactly why the surface has to be
* asked rather than inferred from the number.
*/
export function readRungFor(
frame: LaneFrame,
surface: LaneSurface,
bpPerUnit = 1,
nameBand = NAME_BAND,
): ReadRung {
if (surface !== 'browser') return 'none'
const perBase = basePixels(frame) / Math.max(1e-9, bpPerUnit)
const rung = perBase >= LETTER_MIN_PIXELS ? 'bases' : perBase >= READ_MIN_PIXELS / AVERAGE_READ ? 'reads' : 'none'
if (rung === 'none') return 'none'
// Zoom is not the only thing that decides this. The name strip takes a fixed
// height off the top, so a lane dragged short enough has a pile band that can
// hold nothing — and the pile is what this lane *is*. Answering `reads` there
// drew an empty lane and still spent a whole BAM window on it, so zooming in
// made the picture disappear.
return rowsIn(pileBands(frame, nameBand)[1]) >= 1 ? rung : 'none'
}
/**
* The read length the rung threshold is expressed against.
*
* The switch is about whether a *read* is wide enough to be a shape rather than
* a mark, and a read's width is its length times the pixels per base. A hundred
* is the short-read length this feature is scoped to (§8.13); getting it wrong
* moves the switch by a factor of two, which a reader corrects with one scroll.
*/
const AVERAGE_READ = 100
/** How a pile is painted. */
export interface ReadPaint {
/** One colour per category in `pile.groups`. */
colours: readonly string[]
/** Thickness of one read row, in pixels. */
rowHeight: number
/** Gap between rows. */
rowGap: number
/**
* How a template is laid out and what is drawn between its two ends.
*
* `pairs` draws both reads on one row with a dotted thread across the gap —
* the default, because a pair *is* one fragment and two blocks a row apart
* joined by nothing read as two unrelated reads. `fragments` fills the gap
* instead, for a reader who wants the fragment as one object. `reads` packs
* every record on its own, which is what a single-ended library wants.
*/
layout: PairLayout
/** Draw mismatching bases, where the file gave any. */
diffs: boolean
opacity: number
font: string
/** Ink for the marks that are not a category: gaps, clips, outlines. */
guideColour: string
/**
* Draw each read's base-modification calls of this code over it (§8.13),
* where the pile carries them: modified at or above `threshold`, unmodified
* at or below its complement, each as sure as its probability says.
* Absent draws none, and the mismatch marks are drawn instead.
*/
mods?: { code: string; threshold: number }
}
/**
* The inks of a pile coloured by base modification (§8.13).
*
* Red and blue because that is the pair every reader of these pictures has
* learnt from IGV and from modkit's own plots, and because neither is a read
* category here — under this colouring the reads are drawn in `read`, a grey
* light enough that a blue call on it is still blue. The mismatch marks are
* not drawn under it: they are coloured by base, and a red `T` and a red 5mC
* a column apart would be one ink making two claims.
*/
export const MOD_INK = {
modified: '#d7191c',
unmodified: '#2c7bb6',
read: '#c8c8c8',
} as const
/** The narrowest a call is drawn, in pixels, so one is visible at the zoom reads first appear. */
const MOD_MIN_PIXELS = 2
// ---------------------------------------------------------------------------
// Packing the pile into rows, for the window that is on screen
// ---------------------------------------------------------------------------
/**
* How the reads of a template are laid out together.
*
* `reads` packs every record on its own, which is what a single-ended library
* wants and what this lane did from the start. The other two treat the template
* as the unit — both ends on one row — and differ only in what is drawn between
* them: a thread, or ink.
*/
/** Where every read of a window goes, packed for the window on screen. */
export interface PileLayout {
/** One row per read of the pile it belongs to; `-1` for a read left out. */
row: Int16Array
/** Rows the packing used, which may exceed what the band can draw. */
rows: number
/** Reads placed at all — those overlapping the visible window. */
placed: number
/** …of which this many landed past the last row the band draws. */
hidden: number
}
/**
* The gap between two reads on one row, in **pixels**.
*
* Pixels rather than base pairs, which is what the worker's packer used. A gap
* of three bases is a third of a pixel at 10 bases per pixel — so two reads a
* hundred bases apart were drawn touching, and a row read as one long fragment.
* That is the whole reason a reader cannot tell where one read ends here.
*/
const ROW_PAD = 2
/**
* Pack a window's reads into rows, for the window that is on screen.
*
* ## Why this is not the worker's job
*
* It used to be, and the packing came back on the wire in `ReadPile.row`. Three
* things were wrong with that and all three are visible on a real file:
*
* **The rows were packed for the window that was *fetched*.** That window is
* three view-widths (`ReadCache.FETCH_PAD`), so a reader who zooms in is shown
* a packing made for a picture three times wider, and the rows it needed.
*
* **A window read as several byte spans came back as several piles, each
* numbering its rows from zero.** Drawn into one band they collided, and two
* reads a chunk boundary apart were drawn on top of each other. Packing every
* pile of the window into one row space is what fixes that, and it can only be
* done where all of them are in hand.
*
* **A template cannot be packed as a unit in the worker.** The mate join is
* resolved there, but which reads share a row is a question about the picture —
* it changes with a switch in the settings card — and re-fetching a window to
* answer it would be a BAM read for a drawing decision.
*
* What is given up is row *stability under a pan*: a read can change row when
* the window moves, where the worker's packing held it still for as long as the
* bytes were in hand. That trade is worth taking because the old stability was
* already a half-truth — the packer only ever saw the reads that survived
* thinning, so any change of budget re-packed everything anyway — and because
* a row that is stable but wrong is not the better failure.
*
* ## What it does
*
* Greedy first fit over the units in coordinate order, which is what makes the
* rows compact and the picture stable left to right. Units are read extents
* including their soft clips, because a clip is drawn and two of them
* overlapping would be two reads drawn over each other.
*
* Reads outside `[from, to)` are left out entirely — `row = -1` — so the rows
* count what is on screen and nothing else.
*/
export function packPile(
piles: readonly ReadPile[],
axis: LocusAxis,
frame: LaneFrame,
from: number,
to: number,
layout: PairLayout,
rowsDrawn: number,
): PileLayout[] {
const out: PileLayout[] = piles.map((pile) => ({
row: new Int16Array(pile.length).fill(-1),
rows: 0,
placed: 0,
hidden: 0,
}))
// One unit per thing that occupies a row: a read, or a whole template where
// the layout asks for that. Collected across every pile first, because they
// share one row space — see the docblock.
const units: Array<{ pile: number; a: number; b: number; start: number; end: number }> = []
for (let p = 0; p < piles.length; p++) {
const pile = piles[p]
const segment = pileSegment(axis, pile)
if (segment === null) continue
const unitOf = (base: number): number => unitAt(segment, base)
const paired = layout !== 'reads'
for (let i = 0; i < pile.length; i++) {
const mate = paired ? pile.mate[i] : -1
// Once per template, from its left-hand end: the other end is placed with
// it, so meeting it again is not a second unit.
if (mate >= 0 && mate < i) continue
let lo = pile.refStart[i] - pile.clipStart[i]
let hi = pile.refEnd[i] + pile.clipEnd[i]
if (mate > i) {
lo = Math.min(lo, pile.refStart[mate] - pile.clipStart[mate])
hi = Math.max(hi, pile.refEnd[mate] + pile.clipEnd[mate])
}
const start = unitOf(lo)
const end = unitOf(hi)
// Off screen entirely. The pad is fetched so a pan is free, not so that
// it is drawn — and counting it would make the rows and the caption
// describe a picture three times wider than the one on the screen.
if (end <= from || start >= to) continue
units.push({ pile: p, a: i, b: mate > i ? mate : -1, start, end })
}
}
// Coordinate order, because greedy first fit is only compact over a sorted
// stream. A pile arrives sorted, but two piles interleave and a template's
// extent is not its first read's.
units.sort((one, two) => one.start - two.start || one.end - two.end)
// The gap, in axis units, from a gap in pixels. `toPixel` is affine, so one
// subtraction settles the scale for the whole window.
const perUnit = Math.abs(frame.toPixel(1) - frame.toPixel(0))
const gap = perUnit > 0 ? ROW_PAD / perUnit : 0
const ends: number[] = []
for (const unit of units) {
let row = ends.length
for (let r = 0; r < ends.length; r++) {
if (ends[r] + gap <= unit.start) {
row = r
break
}
}
if (row === ends.length) ends.push(unit.end)
else ends[row] = unit.end
const held = out[unit.pile]
held.row[unit.a] = row
held.placed++
if (row >= rowsDrawn) held.hidden++
if (unit.b >= 0) {
held.row[unit.b] = row
held.placed++
if (row >= rowsDrawn) held.hidden++
}
}
for (const held of out) held.rows = ends.length
return out
}
/**
* Draw one window of reads into a band.
*
* Returns the rows actually drawn, so a caller can say when a pile was taller
* than its lane.
*/
export function drawReads(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
axis: LocusAxis,
pile: ReadPile,
placed: PileLayout,
paint: ReadPaint,
rung: ReadRung,
): number {
const segment = pileSegment(axis, pile)
if (segment === null) return 0
// The same conversion `profileOf` makes, and it has to be the same one: a
// read and the coverage above it disagreeing by half a pixel is a pile that
// does not line up with its own summary.
const at = (base: number): number => frame.toPixel(unitAt(segment, base))
const perBase = Math.abs(at(1) - at(0))
ctx.save()
ctx.globalAlpha = paint.opacity
const step = paint.rowHeight + paint.rowGap
const rowsDrawn = rowsAcross(frame.thickness, paint.rowHeight, paint.rowGap)
// The code's number in *this* pile's table — each pile numbers its own.
const modIndex = paint.mods === undefined ? -1 : (pile.mods?.codes.indexOf(paint.mods.code) ?? -1)
// Pair lines first, so a read is never drawn under the thread joining it to
// its mate — the line is context and the reads are the subject.
if (paint.layout !== 'reads') {
drawPairs(ctx, frame, pile, placed, paint, at, step, rowsDrawn)
}
for (let i = 0; i < pile.length; i++) {
const row = placed.row[i]
if (row < 0 || row >= rowsDrawn) continue
const across = row * step
const colour = paint.colours[pile.group[i]] ?? paint.colours[0] ?? '#4478b8'
// The soft clips, outside the aligned extent and faint: they are what the
// aligner could not place, not what it placed somewhere.
if (pile.clipStart[i] > 0 || pile.clipEnd[i] > 0) {
ctx.globalAlpha = paint.opacity * 0.3
if (pile.clipStart[i] > 0) {
fill(ctx, frame, at(pile.refStart[i] - pile.clipStart[i]), at(pile.refStart[i]), across, paint.rowHeight, colour)
}
if (pile.clipEnd[i] > 0) {
fill(ctx, frame, at(pile.refEnd[i]), at(pile.refEnd[i] + pile.clipEnd[i]), across, paint.rowHeight, colour)
}
ctx.globalAlpha = paint.opacity
}
drawOne(ctx, frame, pile, i, at, across, paint, colour)
if (paint.mods !== undefined) {
if (modIndex >= 0) drawMods(ctx, frame, pile, i, at, across, paint, modIndex, paint.mods.threshold)
} else if (paint.diffs && rung !== 'none') {
drawDiffs(ctx, frame, pile, i, at, across, paint, perBase, rung)
}
}
ctx.restore()
return rowsDrawn
}
/**
* The read under a canvas point, or `null`.
*
* The inverse of {@link drawReads}, and it has to be built out of the same two
* conversions — the axis one and `laneRect`'s — or a click lands on the read
* above the one that was pointed at. That is the reason it lives here beside
* the drawing rather than in the view: the two answers are one piece of
* geometry, and §8.4 says a lane's geometry is decided in one place.
*
* The *last* match wins, as `featureAt` does and for the same reason: within a
* row the reads are in axis order and later ones paint over earlier ones, so
* the one on top is the one that was clicked.
*
* Soft clips are inside the target. They are drawn, faintly, outside the
* aligned extent — and a reader who clicks the faint part is asking about the
* read it belongs to, not about the gap behind it.
*/
export function readAt(
frame: LaneFrame,
axis: LocusAxis,
pile: ReadPile,
placed: PileLayout,
rowHeight: number,
rowGap: number,
x: number,
y: number,
): number | null {
const segment = pileSegment(axis, pile)
if (segment === null) return null
const along = laneIsHorizontal(frame.orientation) ? x : y
const across = canvasToAcross(frame, laneIsHorizontal(frame.orientation) ? y : x)
if (across < 0 || across > frame.thickness) return null
// …and the same bound on the *other* axis, which the paint gets for free from
// `clipLane` and an inverse does not. Without it a click in the name column —
// a strip at least fifty pixels wide, whose documented answer is "reveal this
// track" — lands on a read that begins off the left edge of the view. The
// window is fetched a whole view-width wider on each side, so those reads are
// there in quantity.
const from = Math.min(frame.alongFrom, frame.alongTo)
const to = Math.max(frame.alongFrom, frame.alongTo)
if (along < from || along > to) return null
// The gap below a row belongs to that row. It is two pixels and a pointer is
// not that accurate, so treating it as a miss would make every third click on
// a dense pile do nothing.
const row = Math.floor(across / (rowHeight + rowGap))
// …but not the strip below the *last* drawn row, which `drawReads` leaves
// empty when the band does not divide evenly. A click there would open a card
// for a read that is not on the screen, which is the one way a hit test can
// be wrong and look right.
if (row >= rowsAcross(frame.thickness, rowHeight, rowGap)) return null
const at = (base: number): number => frame.toPixel(unitAt(segment, base))
let found: number | null = null
for (let i = 0; i < pile.length; i++) {
if (placed.row[i] !== row) continue
// A read narrower than a pixel is still a target: the drawn block is
// rounded to one, so a hit area measured exactly would be unhittable at the
// zoom where reads first appear.
const a = at(pile.refStart[i] - pile.clipStart[i])
const b = at(pile.refEnd[i] + pile.clipEnd[i])
if (along < Math.min(a, b) - 1 || along > Math.max(a, b) + 1) continue
found = i
}
return found
}
/**
* One read: its blocks, its gaps and its indels.
*
* Walks the CIGAR rather than filling the extent, because the extent is the one
* thing about a read that is *never* the interesting part.
*/
function drawOne(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
pile: ReadPile,
i: number,
at: (base: number) => number,
across: number,
paint: ReadPaint,
colour: string,
): void {
let refPos = pile.refStart[i]
const from = pile.opAt[i]
const to = pile.opAt[i + 1]
const middle = across + paint.rowHeight / 2
for (let op = from; op < to; op++) {
const code = pile.opCode[op]
const length = pile.opLen[op]
if (code === 0 || code === 7 || code === 8) {
fill(ctx, frame, at(refPos), at(refPos + length), across, paint.rowHeight, colour)
refPos += length
continue
}
if (code === 2) {
// A deletion. The read spans it and says it is absent, so it gets a line
// rather than a gap: a gap would read as "no read here".
line(ctx, frame, at(refPos), at(refPos + length), middle, paint.guideColour, 1.5)
refPos += length
continue
}
if (code === 3) {
// A spliced gap. The read says *nothing* about what it skipped, so the
// line is thinner and lighter than a deletion's — the difference between
// "not there" and "not observed" is most of what an RNA-seq pile is for.
line(ctx, frame, at(refPos), at(refPos + length), middle, paint.guideColour, 0.75)
refPos += length
continue
}
if (code === 1) {
// An insertion has no width on the reference at all, so it is a tick
// *between* two bases rather than a block of any length.
const x = at(refPos)
ctx.save()
ctx.strokeStyle = paint.guideColour
ctx.lineWidth = 1.5
ctx.beginPath()
ctx.moveTo(laneX(frame, x, across), laneY(frame, x, across))
ctx.lineTo(laneX(frame, x, across + paint.rowHeight), laneY(frame, x, across + paint.rowHeight))
ctx.stroke()
ctx.restore()
continue
}
// `S`, `H` and `P` move along the read, never along the reference.
}
// A supplementary alignment is outlined, and nothing else is. It is one piece
// of a molecule the aligner split across a breakpoint, so it must be readable
// *as* a piece — a plain block would say "another read here", which is the
// one thing it is not. An outline rather than a fainter fill, because faint
// is already what a soft clip means on this lane and two faint things a row
// apart cannot be told apart.
if ((pile.flags[i] & SUPPLEMENTARY) !== 0) {
const [x, y, w, h] = laneRect(
frame,
at(pile.refStart[i]),
at(pile.refEnd[i]),
across,
across + paint.rowHeight,
)
ctx.save()
ctx.strokeStyle = paint.guideColour
ctx.lineWidth = 1
ctx.strokeRect(x + 0.5, y + 0.5, Math.max(1, w - 1), Math.max(1, h - 1))
ctx.restore()
}
}
/** Mismatching bases: a coloured column, and a letter once one fits. */
function drawDiffs(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
pile: ReadPile,
i: number,
at: (base: number) => number,
across: number,
paint: ReadPaint,
perBase: number,
rung: ReadRung,
): void {
const from = pile.diffAt[i]
const to = pile.diffAt[i + 1]
if (to <= from) return
const letters = rung === 'bases' && perBase >= LETTER_MIN_PIXELS && paint.rowHeight >= 8
for (let d = from; d < to; d++) {
const base = pile.diffBase[d]
const colour = BASE_COLOURS[base] ?? BASE_COLOURS[4]
const x0 = at(pile.diffPos[d])
const x1 = at(pile.diffPos[d] + 1)
fill(ctx, frame, x0, x1, across, paint.rowHeight, colour)
if (!letters) continue
ctx.save()
ctx.fillStyle = '#ffffff'
ctx.font = paint.font
ctx.textAlign = 'center'
ctx.textBaseline = 'middle'
const mid = (x0 + x1) / 2
const centre = across + paint.rowHeight / 2
ctx.fillText(BASE_LETTERS[base] ?? 'N', laneX(frame, mid, centre), laneY(frame, mid, centre))
ctx.restore()
}
}
/**
* One read's modification calls of one code: a column per call, red or blue,
* as opaque as the caller was sure.
*
* Alpha runs from a sixth at a call that only just cleared the threshold to
* whole at a certain one — so a stretch of confident calls reads as solid
* colour and a stretch of coin-flips as a wash, which is the difference a
* reader is looking for between a methylated island and a noisy model.
*/
function drawMods(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
pile: ReadPile,
i: number,
at: (base: number) => number,
across: number,
paint: ReadPaint,
code: number,
threshold: number,
): void {
const mods = pile.mods
if (mods === undefined) return
const from = mods.at[i]
const to = mods.at[i + 1]
for (let k = from; k < to; k++) {
if (mods.code[k] !== code) continue
const state = modStateOf(mods.prob[k], threshold)
if (state < 0) continue
const p = probabilityOf(mods.prob[k])
const sure = state === 1 ? p : 1 - p
ctx.globalAlpha = paint.opacity * (1 / 6 + (5 / 6) * Math.max(0, (sure - 0.5) * 2))
let x0 = at(mods.pos[k])
let x1 = at(mods.pos[k] + 1)
if (Math.abs(x1 - x0) < MOD_MIN_PIXELS) {
const mid = (x0 + x1) / 2
x0 = mid - MOD_MIN_PIXELS / 2
x1 = mid + MOD_MIN_PIXELS / 2
}
fill(ctx, frame, x0, x1, across, paint.rowHeight, state === 1 ? MOD_INK.modified : MOD_INK.unmodified)
}
ctx.globalAlpha = paint.opacity
}
/**
* The modification calls a read makes at the base nearest a reference position.
*
* The readout's question, answered from the pile the lane drew. The nearest
* call **of the code drawn** within `reach` bases of `pos` decides the base —
* so a pointer a pixel off a one-base column still lands on it, and does not
* land instead on an invisible implicit call of another code a base closer —
* and then every code's call at that base is returned, the drawn one first,
* so a cytosine carrying both a 5mC and a 5hmC call names both.
*/
export function modsNear(
pile: ReadPile,
i: number,
pos: number,
reach: number,
code?: string,
): Array<{ pos: number; code: string; prob: number; byte: number }> {
const mods = pile.mods
if (mods === undefined) return []
const drawn = code === undefined ? -1 : mods.codes.indexOf(code)
if (code !== undefined && drawn < 0) return []
let best = -1
let distance = Number.POSITIVE_INFINITY
for (let k = mods.at[i]; k < mods.at[i + 1]; k++) {
if (drawn >= 0 && mods.code[k] !== drawn) continue
const off = Math.abs(mods.pos[k] + 0.5 - pos)
if (off <= reach && off < distance) {
distance = off
best = mods.pos[k]
}
}
if (best < 0) return []
const out: Array<{ pos: number; code: string; prob: number; byte: number }> = []
for (let k = mods.at[i]; k < mods.at[i + 1]; k++) {
if (mods.pos[k] !== best) continue
out.push({
pos: mods.pos[k],
code: mods.codes[mods.code[k]] ?? '',
prob: probabilityOf(mods.prob[k]),
byte: mods.prob[k],
})
}
if (code !== undefined) out.sort((a, b) => Number(b.code === code) - Number(a.code === code))
return out
}
/** The thread joining the two ends of one template. */
function drawPairs(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
pile: ReadPile,
placed: PileLayout,
paint: ReadPaint,
at: (base: number) => number,
step: number,
rowsDrawn: number,
): void {
const fragment = paint.layout === 'fragments'
ctx.save()
// A thread is context and is drawn faintly; a fragment body is the subject
// and is drawn as the read is, because in that layout the gap is not a gap —
// it is the part of the fragment nobody sequenced.
ctx.globalAlpha = paint.opacity * (fragment ? 0.55 : 0.45)
if (!fragment) {
// Dotted, and this is the whole difference between a pair that reads as a
// pair and one that reads as a fragment: a solid rule between two blocks on
// one row is indistinguishable from a fragment drawn through. The dashes
// are in pixels, so they are the same length at every zoom.
ctx.setLineDash([2, 3])
}
for (let i = 0; i < pile.length; i++) {
const mate = pile.mate[i]
// Once per pair, from the left-hand end — otherwise every line is drawn
// twice, which is visible wherever the lines are translucent.
if (mate <= i) continue
const row = placed.row[i]
if (row < 0 || row >= rowsDrawn) continue
const gapFrom = Math.min(pile.refEnd[i], pile.refEnd[mate])
const gapTo = Math.max(pile.refStart[i], pile.refStart[mate])
if (gapTo <= gapFrom) continue
const across = row * step
if (fragment) {
const colour = paint.colours[pile.group[i]] ?? paint.colours[0] ?? '#4478b8'
fill(ctx, frame, at(gapFrom), at(gapTo), across, paint.rowHeight, colour)
continue
}
line(ctx, frame, at(gapFrom), at(gapTo), across + paint.rowHeight / 2, paint.guideColour, 1)
}
ctx.setLineDash([])
ctx.restore()
}
/** A filled block in lane coordinates. */
function fill(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
along0: number,
along1: number,
across: number,
height: number,
colour: string,
): void {
ctx.fillStyle = colour
const [x, y, w, h] = laneRect(frame, along0, along1, across, across + height)
ctx.fillRect(x, y, w, h)
}
/** A horizontal rule along the read's own middle. */
function line(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
along0: number,
along1: number,
across: number,
colour: string,
width: number,
): void {
ctx.save()
ctx.strokeStyle = colour
ctx.lineWidth = width
ctx.beginPath()
ctx.moveTo(laneX(frame, along0, across), laneY(frame, along0, across))
ctx.lineTo(laneX(frame, along1, across), laneY(frame, along1, across))
ctx.stroke()
ctx.restore()
}
/**
* Room kept clear at the top of a pile lane for its own name and detail, at the
* reader's default text size.
*
* Every other lane draws its label *over* its data, with a halo, and that works
* because a track is low wherever it is low — there is usually somewhere for
* two lines of text to sit. A pile has no such place: it fills the lane and is
* dense by construction, so a label over it is a label read through ink.
* Reserving the strip costs two rows of reads and is the difference between a
* lane whose name can be read and one whose name is decoration.
*
* Two lines, because a pile lane writes both: its name, and how many reads are
* in the window. Thirty pixels held only the first, and the second came out
* through the top row of reads — which is exactly the failure the strip exists
* to prevent. The number is `nameTop + detailDrop + nameLine` from
* `render/laneLabel.ts`: where the first line's centre goes, how far the detail
* drops below it, and one line's room under that.
*
* A *default* rather than the number, because those three scale with the
* reader's text size and this module cannot see it — {@link pileBands} takes
* the strip it should keep, and `BrowserView` computes it from the very
* constants it hands `render/laneLabel.ts`. A constant here would write over a
* reader who made the type larger; this one is what that sum comes to at the
* default size, and it is what every caller that draws no label uses.
*/
export const NAME_BAND = 36
/** Gap between the name strip and the pile, so they read as two and not one. */
export const BAND_GAP = 3
/** One read row, and the gap under it. */
export const READ_ROW = 7
export const READ_ROW_GAP = 2
/**
* How many read rows a lane has room for.
*
* What is left under the name strip, which is what the worker thins the pile
* against. A lane too short for a single row still asks for one: the
* alternative is a request for zero reads, and a pile of none is
* indistinguishable from a failure.
*/
export function rowsFor(frame: LaneFrame, nameBand = NAME_BAND): number {
return Math.max(1, rowsIn(pileBands(frame, nameBand)[1]))
}
/**
* The lane's two bands: the name strip, and the pile under it.
*
* One function because §8.4 means it: the paint lays these out, the row budget
* sent to the worker is measured against the second of them, and the hit test
* inverts it. Three readings of one split, and when they were three
* *expressions* of it the budget over-stated the pile by a gap.
*
* `nameBand` is a thickness rather than a "is it labelled" flag, because the
* strip's right size is the label's own metrics and those live on the surface
* drawing it. Zero is a surface that writes no text — a band of no thickness
* rather than a part that is absent, so every caller can index the pair the
* same way.
*
* It used to be four bands — a name strip, a depth curve and a consensus above
* the pile — and every one of those is now a question this lane does not ask.
* The depth is a row of its own beside this one (§8.13); the consensus is gone.
* A band is not something a reader resizes any more, because a *lane* is.
*/
export function pileBands(frame: LaneFrame, nameBand = NAME_BAND): [LaneFrame, LaneFrame] {
return laneBands(
frame,
[{ fixed: Math.max(0, nameBand) }, { fill: true }],
BAND_GAP,
) as [LaneFrame, LaneFrame]
}
/**
* How many rows of reads a band of this thickness draws.
*
* The one expression of it — genuinely one, now: the budget, {@link drawReads}
* and {@link readAt} all call this rather than inlining the arithmetic, which
* they did until the doc above said they did not. The row height and gap are
* arguments because the paint takes them from `ReadPaint` rather than from the
* module constants.
*
* The `+ rowGap` is not a fudge: the last row needs no gap under it, so a band
* of exactly `n * row + (n - 1) * gap` holds `n` rows.
*/
export function rowsAcross(thickness: number, rowHeight: number, rowGap: number): number {
return Math.max(0, Math.floor((thickness + rowGap) / (rowHeight + rowGap)))
}
function rowsIn(band: LaneFrame): number {
return rowsAcross(band.thickness, READ_ROW, READ_ROW_GAP)
}
/**
* A colour per category, from the lane's own colour.
*
* The lane's colour is what a reader chose and what the swatch on its row
* shows, so the first category keeps it exactly and the rest are rotations of
* its hue — which keeps a two-category colouring (the strands) legible as *one
* track drawn two ways* rather than as two unrelated tracks.
*/
export function readColoursFor(
window: { piles: readonly ReadPile[] },
colour: string,
): string[] {
return readPalette(window.piles[0]?.groups ?? ['reads'], colour)
}
/**
* The palette for a set of categories, from the lane's own colour.
*
* Split out of {@link readColoursFor} so the settings card can draw the same
* key without a pile in hand: the categories are a pure function of the
* colouring (`groupsFor`), so a legend built from them cannot disagree with
* the picture — which a second hand-written palette eventually would.
*/
export function readPalette(groups: readonly string[], colour: string): string[] {
if (groups.length <= 1) return [colour]
return groups.map((_, i) =>
i === 0 ? colour : rotateHue(colour, (i * 360) / (groups.length + 1)),
)
}
/**
* The line under an alignment lane's name.
*
* Says what the pile *is* rather than repeating the coverage axis above it, and
* names the two things a reader cannot see: that reads were dropped to fit, and
* where the mismatch colouring came from — because "no mismatches here" and
* "this file cannot tell me" are the same empty picture (§8.13).
*/
export function pileDetail(
window: {
kept: number
total: number
capped: boolean
diffs: string
note?: string
},
placed: readonly PileLayout[] = [],
/** Under a colouring by base modification, the code drawn and its name. */
mods?: { label: string; calls: number },
): string {
if (window.note !== undefined) return window.note
// What is on the screen, not what came back. The reply covers three
// view-widths, so its counts describe a picture the reader is not looking at
// — and they do not move when the view zooms inside the window that was
// fetched, which is how a caption that says "203 of 394" ends up over a
// drawing of thirty.
const here = placed.reduce((sum, one) => sum + one.placed, 0)
const hidden = placed.reduce((sum, one) => sum + one.hidden, 0)
const reads =
placed.length === 0
? window.capped
? `${window.kept.toLocaleString()} of ${window.total.toLocaleString()} reads`
: `${window.kept.toLocaleString()} reads`
: hidden > 0
? // The one number the lane owed a reader and never gave: a pile taller
// than its band drops its tail silently, and a caption that counted
// the dropped reads as drawn is why a peak of depth forty looked like
// a peak of depth nine.
`${(here - hidden).toLocaleString()} of ${here.toLocaleString()} reads — taller lane for the rest`
: window.capped
? `${here.toLocaleString()} reads, thinned`
: `${here.toLocaleString()} reads`
// What the colours are of, in place of where the mismatches came from: they
// are not drawn under this colouring, and "no MM/ML tags here" is the one
// thing a reader of a plain grey pile needs told.
if (mods !== undefined) {
return `${reads} · ${mods.calls === 0 ? 'no MM/ML calls here' : mods.label}`
}
const diffs =
window.diffs === 'none'
? 'no reference to compare'
: window.diffs === 'md'
? 'MD'
: window.diffs === 'cigar'
? '=/X'
: 'reference'
return `${reads} · ${diffs}`
}
|