Press n or j to go to the next uncovered block, b, p or k for the previous block.
| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | 2x 61x 61x 61x 2x 2x 2x 2x 2x 2x 2x 121x 121x 121x 41x 121x 121x 9x 9x 9x 9x 121x 26x 121x 7x 121x 6x 1x 5x 121x 1x 121x 121x 12x 121x 5x 121x 4x 121x 10x 10x 10x 9x 1x 10x 121x 121x 121x | /**
* A step in words, as the stage's history lists it and the console writes it
* (SPECS §27.2): what was done, to which stretch, in the display form of
* §26.1 — 1-based, grouped — and the names the sequences had when it was done,
* which is what a step is recorded in.
*/
import type { AsideReason, EditStep } from '../genome/edit'
import { formatLocus, formatPosition } from '../genome/assembly'
function span(sequence: string, from: number, to: number): string {
return formatLocus({ contig: sequence, start: from, end: to })
}
const WHY: Record<AsideReason, string> = {
debris: 'debris',
contaminant: 'a contaminant',
haplotig: 'a haplotig',
unplaced: 'unplaced',
}
/** One line for a step. */
export function stepText(step: EditStep): string {
switch (step.op) {
case 'cut':
return `cut ${step.sequence} before ${(step.at + 1).toLocaleString('en-US')}`
case 'invert':
return `turn ${span(step.sequence, step.from, step.to)}`
case 'move':
case 'duplicate': {
const verb = step.op === 'move' ? 'move' : 'copy'
// A place between two bases, named by the base before it — or, at the
// very start, by the one after: never a position past a sequence's end.
const where = step.at === 0 ? `before ${formatPosition(step.into, 0)}` : `after ${formatPosition(step.into, step.at - 1)}`
return `${verb} ${span(step.sequence, step.from, step.to)} ${where}${step.strand === -1 ? ', turned' : ''}`
}
case 'join':
return `join ${step.a}’s ${step.aEnd} to ${step.b}’s ${step.bEnd}${step.gap > 0 ? `, ${step.gap.toLocaleString('en-US')} N between` : ''}`
case 'split':
return `split ${step.sequence} before ${(step.at + 1).toLocaleString('en-US')}`
case 'aside':
// Sent to another genome of the metagenome, it says which (§27.10).
return step.genome !== undefined && step.genome !== ''
? `send ${span(step.sequence, step.from, step.to)} to ${step.genome}`
: `set aside ${span(step.sequence, step.from, step.to)} as ${WHY[step.why]}`
case 'bring':
return `bring in ${step.sequence}`
case 'rotate':
return `start ${step.sequence} at ${(step.at + 1).toLocaleString('en-US')}`
case 'rename':
return `rename ${step.sequence} to ${step.name}`
case 'reorder':
return 'reorder the sequences'
case 'restore':
return `put back ${span(step.sequence, step.start, step.end)}`
case 'place': {
const where = step.before === null ? 'last' : `before ${step.before}`
const turned = step.strand === -1 ? ', turned' : ''
return step.whole === true
? `put ${step.sequence} ${where}${turned}`
: `make ${span(step.sequence, step.from, step.to)} a sequence of its own, ${where}${turned}`
}
case 'layout': {
const count = step.sequences.length
return `lay out as in ${step.from} · ${count.toLocaleString('en-US')} sequence${count === 1 ? '' : 's'}`
}
}
}
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