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plugins/alignments/src/CramAdapter/__snapshots__/util.test.ts.snap
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,3 @@ | ||
| // Jest Snapshot v1, https://goo.gl/fbAQLP | ||
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| exports[`cram read features 1`] = `[]`; |
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| Original file line number | Diff line number | Diff line change |
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| import { readFeaturesToMismatches } from './util' | ||
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| test('cram read features', () => { | ||
| expect( | ||
| readFeaturesToMismatches([{ code: 'i', pos: 5, refPos: 5, data: 'x' }], 0), | ||
| ).toMatchSnapshot() | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
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| import { CramRecord } from '@gmod/cram' | ||
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| type ReadFeatures = CramRecord['readFeatures'] | ||
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| export interface Mismatch { | ||
| qual?: number | ||
| start: number | ||
| length: number | ||
| type: string | ||
| base: string | undefined | ||
| altbase?: string | ||
| seq?: string | ||
| cliplen?: number | ||
| } | ||
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| export function readFeaturesToMismatches( | ||
| readFeatures: ReadFeatures, | ||
| start: number, | ||
| qual?: number[] | null, | ||
| ) { | ||
| if (!readFeatures) { | ||
| return [] | ||
| } | ||
| const mismatches: Mismatch[] = new Array(readFeatures.length) | ||
| let j = 0 | ||
| let insLen = 0 | ||
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| let refPos = 0 | ||
| let sublen = 0 | ||
| let lastPos = start | ||
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| for (let i = 0; i < readFeatures.length; i++) { | ||
| const f = readFeatures[i] | ||
| const { code, pos, data, sub, ref } = f | ||
| sublen = refPos - lastPos | ||
| lastPos = refPos | ||
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| if (sublen && insLen > 0) { | ||
| mismatches[j++] = { | ||
| start: refPos, | ||
| type: 'insertion', | ||
| base: `${insLen}`, | ||
| length: 0, | ||
| } | ||
| insLen = 0 | ||
| } | ||
| refPos = f.refPos - 1 - start | ||
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| if (code === 'X') { | ||
| // substitution | ||
| mismatches[j++] = { | ||
| start: refPos, | ||
| length: 1, | ||
| base: sub, | ||
| qual: qual?.[pos], | ||
| altbase: ref, | ||
| type: 'mismatch', | ||
| } | ||
| } else if (code === 'I') { | ||
| // insertion | ||
| mismatches[j++] = { | ||
| start: refPos, | ||
| type: 'insertion', | ||
| base: `${data.length}`, | ||
| length: 0, | ||
| } | ||
| } else if (code === 'N') { | ||
| // reference skip | ||
| mismatches[j++] = { | ||
| type: 'skip', | ||
| length: data, | ||
| start: refPos, | ||
| base: 'N', | ||
| } | ||
| } else if (code === 'S') { | ||
| // soft clip | ||
| const len = data.length | ||
| mismatches[j++] = { | ||
| start: refPos, | ||
| type: 'softclip', | ||
| base: `S${len}`, | ||
| cliplen: len, | ||
| length: 1, | ||
| } | ||
| } else if (code === 'P') { | ||
| // padding | ||
| } else if (code === 'H') { | ||
| // hard clip | ||
| const len = data | ||
| mismatches[j++] = { | ||
| start: refPos, | ||
| type: 'hardclip', | ||
| base: `H${len}`, | ||
| cliplen: len, | ||
| length: 1, | ||
| } | ||
| } else if (code === 'D') { | ||
| // deletion | ||
| mismatches[j++] = { | ||
| type: 'deletion', | ||
| length: data, | ||
| start: refPos, | ||
| base: '*', | ||
| } | ||
| } else if (code === 'b') { | ||
| // stretch of bases | ||
| } else if (code === 'q') { | ||
| // stretch of qual scores | ||
| } else if (code === 'B') { | ||
| // a pair of [base, qual] | ||
| } else if (code === 'i') { | ||
| // single-base insertion | ||
| // insertion | ||
| insLen++ | ||
| } else if (code === 'Q') { | ||
| // single quality value | ||
| } | ||
| } | ||
| return mismatches.slice(0, j) | ||
| } |