@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/src/MismatchParser/index.test.ts

@@ -1,283 +0,0 @@
-import {
-  getMismatches,
-  cigarToMismatches,
-  mdToMismatches,
-  parseCigar,
-  getNextRefPos,
-  getModificationPositions,
-} from './index'
-
-const seq =
-  'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTT'
-
-// examples come from https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-// and http://seqanswers.com/forums/showthread.php?t=8978
-
-test('cigar to mismatches', () => {
-  expect(cigarToMismatches(parseCigar('56M1D45M'), seq)).toEqual([
-    { start: 56, type: 'deletion', base: '*', length: 1 },
-  ])
-})
-
-test('md to mismatches', () => {
-  const cigarMismatches = cigarToMismatches(parseCigar('56M1D45M'), seq)
-  expect(
-    mdToMismatches('10A80', parseCigar('56M1D45M'), cigarMismatches, seq),
-  ).toEqual([
-    { start: 10, type: 'mismatch', base: 'C', altbase: 'A', length: 1 },
-  ])
-})
-
-describe('get mismatches', () => {
-  it('simple deletion', () => {
-    // simple deletion
-    expect(getMismatches('56M1D45M', '56^A45', seq)).toEqual([
-      { start: 56, type: 'deletion', base: '*', length: 1 },
-    ])
-  })
-
-  it('simple insertion', () => {
-    // simple insertion
-    expect(
-      getMismatches(
-        '89M1I11M',
-        '100',
-        'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTA',
-      ),
-    ).toEqual([{ start: 89, type: 'insertion', base: '1', length: 0 }])
-  })
-
-  it('deletion and a SNP', () => {
-    // contains a deletion and a SNP
-    // read GGGGG--ATTTTTT
-    //      |||||   ||||||
-    //      GGGGGACCTTTTTT
-    expect(getMismatches('5M2D6M', '5^AC0C5', 'GGGGGATTTTTT')).toEqual([
-      { start: 5, type: 'deletion', base: '*', length: 2 },
-      { start: 7, type: 'mismatch', base: 'A', altbase: 'C', length: 1 },
-    ])
-  })
-
-  it('0-length MD entries', () => {
-    // 0-length MD entries, which indicates two SNPs right next to each other
-    // "They generally occur between SNPs, or between a deletion then a SNP."
-    // http://seqanswers.com/forums/showthread.php?t=8978
-    //
-    // read GGGGGCATTTTT
-    //      |||||  |||||
-    // ref  GGGGGACTTTTT
-    expect(getMismatches('12M', '5A0C5', 'GGGGGCATTTTT')).toEqual([
-      { altbase: 'A', base: 'C', length: 1, start: 5, type: 'mismatch' },
-      { altbase: 'C', base: 'A', length: 1, start: 6, type: 'mismatch' },
-    ])
-  })
-
-  it('non-0-length-MD string', () => {
-    // same as above but with the non-0-length MD string
-    // not sure if it is entirely legal, but may appear in the wild
-    expect(getMismatches('12M', '5AC5', 'GGGGGCATTTTT')).toEqual([
-      { altbase: 'A', base: 'C', length: 1, start: 5, type: 'mismatch' },
-      { altbase: 'C', base: 'A', length: 1, start: 6, type: 'mismatch' },
-    ])
-  })
-})
-
-test('basic skip', () => {
-  expect(getMismatches('6M200N6M', '5AC5', 'GGGGGCATTTTT')).toEqual([
-    { base: 'N', length: 200, start: 6, type: 'skip' },
-    { altbase: 'A', base: 'C', length: 1, start: 5, type: 'mismatch' },
-    { altbase: 'C', base: 'A', length: 1, start: 206, type: 'mismatch' },
-  ])
-})
-
-test('vsbuffalo', () => {
-  // https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-  // example 1
-  expect(
-    getMismatches(
-      '89M1I11M',
-      '100',
-      'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA',
-    ),
-  ).toEqual([{ base: '1', length: 0, start: 89, type: 'insertion' }])
-
-  // https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-  // example 2
-  expect(
-    getMismatches(
-      '9M1I91M',
-      '48T42G8',
-      'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA',
-    ),
-  ).toEqual([
-    { base: '1', length: 0, start: 9, type: 'insertion' },
-    {
-      altbase: 'T',
-      base: 'A',
-      length: 1,
-      start: 48,
-      type: 'mismatch',
-    },
-    {
-      altbase: 'G',
-      base: 'A',
-      length: 1,
-      start: 91,
-      type: 'mismatch',
-    },
-  ])
-})
-
-test('more skip', () => {
-  expect(getMismatches('3M200N3M200N3M', '8A', 'GGGGGCATTTTT')).toEqual([
-    { base: 'N', length: 200, start: 3, type: 'skip' },
-    { base: 'N', length: 200, start: 206, type: 'skip' },
-    { altbase: 'A', base: 'T', length: 1, start: 408, type: 'mismatch' },
-  ])
-  expect(
-    getMismatches('31M1I17M1D37M', '6G4C20G1A5C5A1^C3A15G1G15', seq).sort(
-      (a, b) => a.start - b.start,
-    ),
-  ).toMatchInlineSnapshot(`
-    [
-      {
-        "altbase": "G",
-        "base": "A",
-        "length": 1,
-        "qual": undefined,
-        "start": 6,
-        "type": "mismatch",
-      },
-      {
-        "altbase": "C",
-        "base": "A",
-        "length": 1,
-        "qual": undefined,
-        "start": 11,
-        "type": "mismatch",
-      },
-      {
-        "base": "1",
-        "length": 0,
-        "start": 31,
-        "type": "insertion",
-      },
-      {
-        "altbase": "G",
-        "base": "C",
-        "length": 1,
-        "qual": undefined,
-        "start": 32,
-        "type": "mismatch",
-      },
-      {
-        "altbase": "A",
-        "base": "C",
-        "length": 1,
-        "qual": undefined,
-        "start": 34,
-        "type": "mismatch",
-      },
-      {
-        "altbase": "C",
-        "base": "C",
-        "length": 1,
-        "qual": undefined,
-        "start": 40,
-        "type": "mismatch",
-      },
-      {
-        "altbase": "A",
-        "base": "C",
-        "length": 1,
-        "qual": undefined,
-        "start": 46,
-        "type": "mismatch",
-      },
-      {
-        "base": "*",
-        "length": 1,
-        "start": 48,
-        "type": "deletion",
-      },
-      {
-        "altbase": "A",
-        "base": "G",
-        "length": 1,
-        "qual": undefined,
-        "start": 52,
-        "type": "mismatch",
-      },
-      {
-        "altbase": "G",
-        "base": "G",
-        "length": 1,
-        "qual": undefined,
-        "start": 68,
-        "type": "mismatch",
-      },
-      {
-        "altbase": "G",
-        "base": "G",
-        "length": 1,
-        "qual": undefined,
-        "start": 70,
-        "type": "mismatch",
-      },
-    ]
-  `)
-})
-
-test('clipping', () => {
-  expect(getMismatches('200H10M200H', '9A', 'AAAAAAAAAC')).toEqual([
-    { cliplen: 200, base: 'H200', length: 1, start: 0, type: 'hardclip' },
-    { cliplen: 200, base: 'H200', length: 1, start: 10, type: 'hardclip' },
-    { altbase: 'A', base: 'C', length: 1, start: 9, type: 'mismatch' },
-  ])
-
-  expect(getMismatches('10S10M10S', '9A', 'AAAAAAAAAAGGGGGGGGGC')).toEqual([
-    { cliplen: 10, base: 'S10', length: 1, start: 0, type: 'softclip' },
-    { cliplen: 10, base: 'S10', length: 1, start: 10, type: 'softclip' },
-    { altbase: 'A', base: 'C', length: 1, start: 9, type: 'mismatch' },
-  ])
-})
-
-test('getNextRefPos test 1', () => {
-  const cigar = parseCigar('10S10M1I4M1D15M')
-  const iter = getNextRefPos(cigar, [5, 10, 15, 20, 25, 30, 35])
-  expect([...iter]).toEqual([0, 5, 15, 20, 25])
-})
-test('getNextRefPos test 2', () => {
-  const cigar = parseCigar('10S15M')
-  const iter = getNextRefPos(cigar, [5, 10, 15])
-  expect([...iter]).toEqual([0, 5])
-})
-
-test('getModificationPositions', () => {
-  const positions = getModificationPositions(
-    'C+m,2,2,1,4,1',
-    'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA',
-    1,
-  )
-  expect(positions[0]).toEqual({ type: 'm', positions: [6, 17, 20, 31, 34] })
-})
-
-// ? means "modification status of the skipped bases provided."
-test('getModificationPositions with unknown (?)', () => {
-  const positions = getModificationPositions(
-    'C+m?,2,2,1,4,1',
-    'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA',
-    1,
-  )
-  expect(positions[0]).toEqual({ type: 'm', positions: [6, 17, 20, 31, 34] })
-})
-
-// . means "modification status of the skipped bases is low probability"
-test('getModificationPositions with unknown (.)', () => {
-  const positions = getModificationPositions(
-    'C+m.,2,2,1,4,1',
-    'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA',
-    1,
-  )
-  expect(positions[0]).toEqual({ type: 'm', positions: [6, 17, 20, 31, 34] })
-})