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csi.test.ts
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// @ts-nocheck
import { csi, BamFile } from '../src'
import { LocalFile } from 'generic-filehandle'
import FakeRecord from './fakerecord'
class HalfAbortController {
constructor() {
this.signal = { aborted: false }
}
abort() {
this.signal.aborted = true
}
}
describe('bam header', () => {
it('loads volvox-sorted.bam', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/volvox-sorted.bam'),
})
await ti.getHeader()
expect(ti.header).toEqual('@SQ SN:ctgA LN:50001\n')
expect(ti.chrToIndex.ctgA).toEqual(0)
expect(ti.indexToChr[0]).toEqual({ refName: 'ctgA', length: 50001 })
const ret = await ti.indexCov('ctgA')
expect(ret).toMatchSnapshot()
})
it('loads volvox-sorted.bam with csi index', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/volvox-sorted.bam'),
csiPath: require.resolve('./data/volvox-sorted.bam.csi'),
})
await ti.getHeader()
expect(ti.header).toEqual('@SQ SN:ctgA LN:50001\n')
expect(ti.chrToIndex.ctgA).toEqual(0)
expect(ti.indexToChr[0]).toEqual({ refName: 'ctgA', length: 50001 })
})
})
describe('bam records', () => {
let ti
beforeEach(() => {
ti = new BamFile({
bamPath: require.resolve('./data/volvox-sorted.bam'),
})
return ti.getHeader()
})
it('gets features from volvox-sorted.bam', async () => {
const records = await ti.getRecordsForRange('ctgA', 0, 1000)
expect(records.length).toEqual(131)
expect(records[0].get('start')).toEqual(2)
expect(records[0].get('end')).toEqual(102)
expect(records[0].get('cigar')).toEqual('100M')
expect(records[0].get('name')).toEqual('ctgA_3_555_0:0:0_2:0:0_102d')
expect(records[0].get('qual')).toEqual(
'17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17',
)
expect(records[0].get('md')).toEqual('100')
expect(records[0].getReadBases()).toEqual(
'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG',
)
})
it('gets features from the end of volvox-sorted.bam', async () => {
const records = await ti.getRecordsForRange('ctgA', 47457, 50001)
expect(records.length).toEqual(473)
})
it('gets out of bounds from volvox-sorted.bam', async () => {
const records = await ti.getRecordsForRange('ctgA', 60000, 70000)
expect(records.length).toEqual(0)
})
it('gets large chunk from volvox-sorted.bam', async () => {
const promises = []
const win = 1000
for (let i = 0; i < 50000; i += win) {
const records = ti.getRecordsForRange('ctgA', i, i + win)
promises.push(records)
}
const recs = await Promise.all(promises)
expect(recs.every(record => record.length > 0)).toBeTruthy()
})
it('gets specific weird chunk of volvox-sorted.bam', async () => {
const records = await ti.getRecordsForRange('ctgA', 32749, 32799)
expect(records.length).toEqual(13)
})
it('gets specific other weird chunk of volvox-sorted.bam', async () => {
const records = await ti.getRecordsForRange('ctgA', 32799, 32849)
expect(records.length).toEqual(11)
})
})
describe('bam deep record check', () => {
it('deep check volvox-sorted.bam', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/volvox-sorted.bam'),
})
await ti.getHeader()
const records = await ti.getRecordsForRange('ctgA', 0, 10)
expect(records).toMatchSnapshot()
})
})
describe('1000 genomes bam check', () => {
it('deep check 1000 genomes', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/1000genomes_hg00096_chr1.bam'),
csiPath: require.resolve('./data/1000genomes_hg00096_chr1.bam.csi'),
})
await ti.getHeader()
const records = await ti.getRecordsForRange('1', 0, 1000)
expect(records).toMatchSnapshot()
})
it('deep check 1000 genomes csi', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/1000genomes_hg00096_chr1.bam'),
})
await ti.getHeader()
const records = await ti.getRecordsForRange('1', 0, 1000)
expect(records).toMatchSnapshot()
})
it('start to deep check 1000 genomes but abort instead', async () => {
const aborter = new HalfAbortController()
const ti = new BamFile({
bamPath: require.resolve('./data/1000genomes_hg00096_chr1.bam'),
csiPath: require.resolve('./data/1000genomes_hg00096_chr1.bam.csi'),
})
const recordsP = ti
.getHeader(aborter.signal)
.then(() =>
ti.getRecordsForRange('1', 0, 1000, { signal: aborter.signal }),
)
aborter.abort()
await expect(recordsP).rejects.toThrow(/aborted/)
})
})
describe('ecoli bam check', () => {
it('check ecoli header and records', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/ecoli_nanopore.bam'),
})
const header = await ti.getHeader()
const records = await ti.getRecordsForRange('ref000001|chr', 0, 100)
expect(header).toMatchSnapshot()
expect(records).toMatchSnapshot()
})
})
describe('BamFile with test_deletion_2_0.snps.bwa_align.sorted.grouped.bam', () => {
let b
beforeEach(async () => {
b = new BamFile({
bamPath: 'test/data/test_deletion_2_0.snps.bwa_align.sorted.grouped.bam',
})
await b.getHeader()
})
it('constructs', () => {
expect(b).toBeTruthy()
})
it('loads some data', async () => {
const features = await b.getRecordsForRange('Chromosome', 17000, 18000)
expect(features.length).toEqual(124)
expect(
features.every(
feature => feature.get('seq_length') === feature.getReadBases().length,
),
).toBeTruthy()
})
})
describe('BamFile tiny', () => {
it('loads some data', async () => {
const b = new BamFile({
bamPath: 'test/data/tiny.bam',
})
await b.getHeader()
const features = await b.getRecordsForRange('22', 30000000, 30010000)
expect(features.length).toEqual(2)
})
})
describe('BamFile secondary', () => {
it('checks secondary', async () => {
const b = new BamFile({
bamPath: 'test/data/secondary.bam',
})
await b.getHeader()
const features = await b.getRecordsForRange('20', 10761157, 10761387)
const dups = features.map(f => f.isDuplicate()).reduce((x, y) => x + y)
expect(dups).toEqual(2)
})
})
describe('BamFile empty', () => {
it('loads but does not crash', async () => {
const b = new BamFile({
bamPath: 'test/data/empty.bam',
})
await b.getHeader()
const features = await b.getRecordsForRange('22', 30000000, 30010000)
expect(features.length).toEqual(0)
})
})
describe('BamFile with B tags', () => {
it('test B tags', async () => {
const b = new BamFile({
bamPath: 'test/data/Btag.bam',
})
await b.getHeader()
const features = await b.getRecordsForRange('chr1', 980654, 981663)
// ZC:B:i,364,359,1,0 ZD:B:f,0.01,0.02,0.03 ZE:B:c,0,1,2,3 ZK:B:s,45,46,47
const ret = features[1].get('ZD').split(',')
expect(features[1].get('ZC')).toEqual('364,359,1,0')
expect(features[1].get('ZE')).toEqual('0,1,2,3')
expect(features[1].get('ZK')).toEqual('45,46,47')
expect(+ret[0]).toBeCloseTo(0.01)
expect(+ret[1]).toBeCloseTo(0.02)
expect(+ret[2]).toBeCloseTo(0.03)
expect(features.length).toEqual(2)
})
})
describe('BamFile with paired ends', () => {
it('paired ends', async () => {
const b = new BamFile({
bamPath: 'test/data/paired.bam',
})
await b.getHeader()
const features = await b.getRecordsForRange('20', 62500, 64500)
const f = features[0]
expect(f._next_refid()).toEqual(19)
expect(f._next_pos()).toEqual(62352)
})
it('read as pairs', async () => {
const b = new BamFile({
bamPath: 'test/data/paired.bam',
})
const p = new BamFile({
bamPath: 'test/data/paired-region.bam',
})
await b.getHeader()
await p.getHeader()
const features = await b.getRecordsForRange('20', 62500, 64500, {
viewAsPairs: true,
})
const features2 = await p.getRecordsForRange('20', 0, 70000)
// expect(features.length).toEqual(features2.length)
expect(features.map(f => f.get('name')).sort()).toEqual(
features2.map(f => f.get('name')).sort(),
)
const f = features[features.length - 1]
const f2 = features2[features2.length - 1]
expect(f.get('start')).toEqual(f2.get('start'))
})
})
describe('BamFile+CSI with large coordinates', () => {
it('use csi', async () => {
const b = new BamFile({
bamPath: 'test/data/large_coords.bam',
csiPath: 'test/data/large_coords.bam.csi',
})
await b.getHeader()
const features = await b.getRecordsForRange(
'ctgA',
1073741824,
1073741824 + 50000,
)
expect(features.length).toEqual(9596)
})
})
describe('Pair orientations', () => {
it('test pair orientations', async () => {
const b1 = new FakeRecord(true, 'F', 'F', 100)
const b2 = new FakeRecord(true, 'F', 'R', 100)
const b3 = new FakeRecord(true, 'R', 'R', 100)
const b4 = new FakeRecord(true, 'R', 'F', 100)
const b5 = new FakeRecord(false, 'F', 'F', 100)
const b6 = new FakeRecord(false, 'F', 'R', 100)
const b7 = new FakeRecord(false, 'R', 'R', 100)
const b8 = new FakeRecord(false, 'R', 'F', 100)
const b9 = new FakeRecord(false, 'F', 'F', -100)
const b10 = new FakeRecord(false, 'F', 'R', -100)
const b11 = new FakeRecord(false, 'R', 'R', -100)
const b12 = new FakeRecord(false, 'R', 'F', -100)
expect(b1.getPairOrientation()).toEqual('F1F2')
expect(b2.getPairOrientation()).toEqual('F1R2')
expect(b3.getPairOrientation()).toEqual('R1R2')
expect(b4.getPairOrientation()).toEqual('R1F2')
expect(b5.getPairOrientation()).toEqual('F2F1')
expect(b6.getPairOrientation()).toEqual('F2R1')
expect(b7.getPairOrientation()).toEqual('R2R1')
expect(b8.getPairOrientation()).toEqual('R2F1')
expect(b9.getPairOrientation()).toEqual('F1F2')
expect(b10.getPairOrientation()).toEqual('R1F2')
expect(b11.getPairOrientation()).toEqual('R1R2')
expect(b12.getPairOrientation()).toEqual('F1R2')
})
})
describe('SAM spec pdf', () => {
it('check parse', async () => {
const b = new BamFile({
bamPath: 'test/data/samspec.bam',
csiPath: 'test/data/samspec.bam.csi',
})
await b.getHeader()
const features = await b.getRecordsForRange('ref', 1, 100)
expect(features.length).toEqual(6)
expect(features[2].get('sa')).toEqual('ref,29,-,6H5M,17,0;')
expect(features[4].get('sa')).toEqual('ref,9,+,5S6M,30,1;')
})
})
describe('trigger range out of bounds file', () => {
it('range error', async () => {
const b = new BamFile({
bamPath: 'test/data/cho.bam',
})
await b.getHeader()
expect(Object.keys(b.chrToIndex).length).toEqual(28751)
})
})
// we cannot determine duplicates as unique because we require dehashing
test('unique id for duplicate features', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/exact_duplicate.bam'),
})
await ti.getHeader()
const ret = await ti.getRecordsForRange('ctgA', 0, 1000)
expect(ret[0].id() !== ret[1].id()).toBeTruthy()
})
test('usage of the chr22 ultralong nanopore', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/chr22_nanopore_subset.bam'),
})
await ti.getHeader()
const ret1 = await ti.getRecordsForRange('22', 16559999, 16564499)
const ret2 = await ti.getRecordsForRange('22', 16564499, 16564999)
const findfeat = k => k.get('name') === '3d509937-5c54-46d7-8dec-c49c7165d2d5'
const [r1, r2] = [ret1, ret2].map(x => x.find(findfeat))
expect(r1.getReadBases()).toEqual(r2.getReadBases())
expect(r1.getReadBases()).toBe(
'TCTTCAGACCCTCGAAACAGTGTTCTGAAATCCTATGGCAGGGAACAACAGAACCCAGCCACTGTGTGCTGGAATCCTGTCTGAGGACAAACATTCAAACACTCATGAAAGTGTTCTGGAATCTTATGTGAGTGATAAGCAATCAGAAACCAGCAGCGGTGCTCTGTAATCCTTTGTGAGGACAAACAGTACACAGAGCAAGTTCTGGAGTTCTATGTGAGGGACAAACTCTCATGACAGCAGCAGTGTTCTGGAATCACTTGTGAGGGCCAAACACTCAGACTTATGCAGCAGTATTTACAGATCTTATGTGTGATGGAAAACACTCTGAACCCAGCAGCAGTGTTCTGGAATCCTATATGAGGAAAAACTCAGAACCTGCAGCAGTGTTCTGGAATCCTTAGTGAGGAGGTATTCAGAACCTCATATCAGTGTTATGGAATCGTATGTGAGGACAAACACTCTGAAACCAGCAGCAGTGTTCTGGAATCCCATGTGAGAGACAAACACGAGAATCCAGCAGCAGTATTCTGGAATCCTATGTGTGAAAACACCCAGAAACCAGCAGCGTAGTACTGGAAGGAAATCTTTGTTAGGGGCTAACATTCAGACACAAGCTGTATTCTGGAATCTATGTGAGGACAAACACTCCTATCAGTAGCAATGTTCTGCAATTCTTTAGCAGCAGACAACATCTTCAGGCCCTCATGCAGCAGTTTCAAAAATTCCACAAGAGTGAGAGATTAAACACTCCAGAACCCAGCAGAAATGCAGGGATCTATGTGAGGGCAAATACTTGGAATCCAGCAGCACTGTTCTTGAAACCTATGTGAGGGACAAGCACTCACAACAGCCACTGTGTACCAGAATCCTATTTGATTGTCAAACACTTCAGACCCTAGTAGAGGAGTGTTCTGGAATCCCTATGTGAAGGACAAACTCTAAATAACCAGCATAGCAGTGCTCTGGAATCTTTGGGAGAGAAAGCATCAGACCCTAGCAGTGTTCTGGGATCCTATGTGAGGGAAAAACATTCCAGACCCGCATAGCAGTGTTTGGAATCTATACGAGTGACAAACACTCAGAACCCACCAGCAGTGTTCTGAATCTTTTTGTGAGGTAAAAACACTCAGACCCTCAAAGCAGTGTTCTGGAATCCTGCGTGATGGAAAAACATTCAGACGTAGCTGTGTTCTGGAATCCTATGTGAGGGAGAAACATTGTGACCCTCATGTAGCATTGTTCTGGAATCCAATATGAGGGACAAACACTCAGAAGCCAGCAGCTGTATTCTGGAATGCCATATTGAGAAAAGACTCCAGAACCCAACAGCAGTGTTCTGGAGATCTATCAAGGAAATAACCCTAGAGATTGGAGCACTGTACTGGAAGTCTTATATTAGGGACACATATTCAGACACTCGTAGAAGTGTTCTGGAATACTATGTGAAAGGACAAACACTAAGAAAACAGCAGCAGGGCTTTGGAATCCTTTGTGAGGACAAAAAAACAGAACCCATCAGCAGTGTTCTGAGAATCATTGTGAGAAAAATGTTTCTAGGTCCTATTAACAGTGTTCTGGAGATCCTATGTGAGGTAAACATTCAGATCCCTCATAGCAGTGGTCTGGAATCGTATGTGAGAGACAAACCCTCACAACCCAGCAGCAGTGTTCTGCAATCCCTATGTGAGCGACGAACATTGAGAACTTCGTAGCAGTGTTCTGATATTCTATGTAGAGCAAACACTCACAACCCGGCAGCACTGCTCTGGAATCGTATGTGAGGACAACAACAGAACCCAGCAGCCGTGTTCTGGAAACCTCGTGAGGGACAAAATCTCAGAGCTCAGCAGCAGTGTTCTGCAATCCTATGTGAGTGACAAATACTCAGAACCCAGCAGCAGTGTTCTGGAATCTTTGTGAGGACAAACACTAGAACCCAGCAGCAGTGTTCTAGAGTCCTTTGTGAGGACAAACATTCAGAAACTCTCTTCCAGTGTTCTGGAATCTTAGGTGAGGGACAAACACACTGAACCCAGCAGCTGTTTTGGAATCCCATGTGAGGCAGAAACACTCAGAACTCAGCAGTGTTCTGGAATCTATGTGAGTGAAAAACACTCAGGAGCCAACAGCAGTGTTCACAGAATCTTTGTGGGCAAACCTTCAAGACCCTAGAATCAGTGTTCTGGAATCCTATGTGATGAACAAACACTCAGAACCCAACAGCAGTGTTTTTGATTCCTTTGTTTTGGAGAAACATTCAGACCATTGTAGCACTGTTCCACTATTCTATGTGAGGGACAAACTCTCAGAACCCAGTAGCAGTGCTAAGTCCTATGTGAGGACAAACACTCAGAACCCAGCAGCAGGGTTCTGGAATCCTATGTGAGGGTCAAGCACTCAGAGGCAGCAGCAGTGTTCTGGAATCCCTATGTGAGGGCTTACTAAGAACCCAGTCACTGTGTGCTGGAATCCTATGTGGGAGAAACATTAGAGACAGTCACTGTGTGCTGGAATCCTATCTCAAGGACAAACATTCAGACCATTGTAGCACTGTTCCGCTATCCCTAGCGAGGGACAAACTCTCAGAACCCAGTAGCAGTGCTCTAGGAATCCTATGTGAGGACAGAAACACTGAACCCAGCAGCAGCAGGAATACTGGAATCCTATGTGAGGTCAAACACTCAGAAGGCAGCAGCAGTATTCTGGAATACATGGCAGGAGAAACATTCAGAACCCAGTGCTGTGTGCTGGAATCCTATGTGAGGGGAGAAACACTCACAACTCAGTCACTATGTGCTGGAATCCTATCTGAGGACAAACATTCAGACATGTAGAAGTGTCCTGGAATCCTATGAGGGACAAACACTGAGAACCCAGCAGCAGAGTTCTAGAATTCTTCGTGAAGACAAACATTCAGACACTCGAAGCAGTGTCCTAGAATCTATGTGAGGACAAACACTTCTAGAACCCAGCAGAATTGTTCTGGAATCCTTTGTGATGGATGAGCATTTGAGCCCTCGTGGCAGTGTTCTGGAAACCTAAGTGAGGGCAAACACTCAGTTGTAGCAGTGTTCTGGAATCCTATGTGACTGACAAACACTCAGAACCCTGAAGCAATGTTATGAAATCCTGTGTGAGTGCAAACACTCAGAACCCACCATCAATGCTCTGCAATCCTATGTGAGGAAAGAAACACTCAGAAACCTGCAGCAGTGTTCTGGAATCTATATATGGGTCAATAATTCAGACCATCATAGCACTGTTCTGGAATGCTCTGTGAGGACAAACATTCAGAAACTTGTAGCAGAGTTCTGGAATCTATGTGAGGGAGAAACCCTCAGAACCTAGCAGTAGTGTTCTGGAATCCTTATGTGAGATAACACTCAAGACCAGCCGCAGTGTTCTGGAATGCTATGTGAGGACAAACACTCAAAACCAAGCAGCAGGATTCTGTTATCTACCATGAGACAAACACTCGAACCCAGCAGAACTGTTATGGAATCTATGTGAGGACAAACACTCACAAACAAGCAGCTTTTGGAATCCCTATGTGAGGAGAAATCTTCAGAACCTAGCAGCAGTGTTCTGGAATCGTATGTGTGGACTTCAGCACACTCAGAACCCAGCAGCATGTTGAGAATGCTATGTGAGGGAGAAACACACAAAACCCACCAGCAGTGTTCTGGTTTAATATATGCGGGACAAACACACAGAACCCAGCAGAAGTGTTCTGTAATCCCATGTGAGGGTCAAACACTCACAAACCAGCAGCAATGTTTTGGAGTCTCTTTGTGAGGGACAAACATTAAACCTCAATAAAGTGCTCTGCAATCTATCAGCGAGGAACAACACTCTACAGGCCCAGCAGCAATGTTTTCGAATCCCATGAAAGGGACAAACACTCAGAACTTCGGCAGCATTTTCTGGAATCCTATGGTGACAAACTCTCAGAACACAGCAGCGGTGTTCTAGAATCACTGTAGGAGACAAACATTCAGAATGATCATAACAGTGTTCTGGTATCTCATGTGAGGACAAACACTCGGAAACCAGCAGCAGTGCTCTGAATTCTTGCAGGACAAACAAACCGAAGAGGTTCTGGAATTACTGTAAAGGACCAAGCACTGAGAACCCAGGAGCAGCGTTCTGGAATCCCATGTGAGGGACAAACGCTCAGAACCCAACAGCAGTGTTCTGTAATCTAATTGAGGACAGACACTCACAGCCCAGCATTGTTCTAGATTCGCTGTGAGGAACCAAGCATTTCAGACCCTCGGCAGTGTTCTGGAATGTTATGTGAGGGACAACCCTCTGAACCCAGCAGGGTTCTGGAATCAGTGAGTGACAAACACTCAAAACCCAGCAGCAGTGTTCCGGAATCCTTTGTGAGGACAAGCTTTCCAAACCTCGAAGCATTGTTATGGAGTCACCTTAGCAACGAGGAACACACTCAGAATCCCGCGCGCAGCGATATGATCTTGTGATGGACAAACATCCAGACACTCTTAGCAGTGTTCTGGAACGCTATGTGATGATTGTAAACCTACAGGCCAGGCAGTGTTCTGGAATCCTCTGTGAGGACAAACACTCAGAACCCAGTAGTAGTGTTCTGGAATCTAATGCATGAGGACAAACACACTAAGAACCCAAGGAGCAGTGTTCTGCAATCTATGAGGGACAAACACTACAGCCCACCAGCATGGCAGTGTTCTAGAATCCTTTGTGAGGAAAAACATTCAGACCATCGAATCAGTGTTCTGGAATCTATATGTGGGGAGACAAACGCTCAGAACCCAGCAGCAGTTTTCTGATCCTTTTCAGACAGACAAACCTTTAGACGATCTTAGCAGTGTTCTGTTATCTATGTAAGGGACAAACACTCAGAACCCAGCAGCAGTGCTCTGGATTCCTTTGTGGGGACGAGCACTTAGAACCCAGGAGCAGTGTTCTGGAATCCTATGTGAGGACAAACACTCAGAATCCAGCAGCAGTGTTCTGGAATCTTAGAGTGAGGACAGACACTCACAACCCAGCAGCAGTGTTCTAGAATCCTTTGTGAGGGACAAACAGCATCAGACCACAGAAGCAGTGTTTCTGGAATCTATGTGAGAGCAAACACTCAGAGACACAGCATCAGTGTTTCACAGAATCCTATCTTGAGTGACAAACTAGAACCAGAACAGTATTCATCCATTGTAGAGGACAAACATTCTGTCTCAGCGAAGCATTTTTCTGGATTCCTATGCTGAGGGACACACTCAGAACCCAGCAGCAGTGTTCTGGAATCCTATGTGTGGGACAAACACTCAGAAACCAGCAGCAGTGTTCTGGAATCCTACCGTGAGGGACAAACACTCAGAACACAGCTACTCTGTACTGGGAATCTATCTGAGTATTGACAACATTCAGACTCTTGCAGAAGTGTTCTGGAATCCTATGTGATGGACAAACACTAACAAACTAGCAGCAGCGCTCTGGAATTCTTTGTGATACAGACGTGTTCAAGGAGCTCTTTAACAGTGTTCTGGAATCGTATGTGAGTACAAACACTCAAAACTCAGCAGCAGTGTTCTGGAATTCTATTTGAGGACAAACTCTCAGAACCCAGCAGCCATGCTGTGAAATGATATGTGGACAGACACTCAGAACCCAACAGCAGAGTTCTGGTATCTAAGTGAGGAACAAACACTCAGAACCCTGCAGAAGTATTCTGGAATCATGTGAGGGACAAACACTCAAAATCCAAGAAGGCAGTGTTCTGGAATCCTATGTGAGGACAAACACTCACACCCTCGAAGTGTTCTGGAATCTATGTGAAGGACAAACACTCAGAACCCAGTAGCAGTGTTCTGGAATCTGGTGTGAAGGACAAGCGTTCAGACTTGCTCGTAGCAGTGATATGGAGTTGCTGTAGAGACAAGCATTCCAGACACACTTATGTTCTGGAATCCTAAGTGAGAGAAACCCTCAAAAACAAGCTGCAGTGTTCTAGGAAATCTATGAAAGGACAATCCCTCAGTATCGAGGCAGTGTTTGGAATCCTATCTGAGGGACAAACACTCAGAACTCAGCAGCAGTGTTCTGGAATCCTGTGTGAAGGAGAAACACTAGAACCCAACAGCAGTGTTCTGATTCCCGAAGTGTGGGACAATCACTCAAAACCCAGCCACTGTGTTCTGGAATCCTATCTGAGGTCAATGTAGGAACCTCGAGGAAGAGTTCTGGAATCCTATGTGAGGGAAAACACTCTGAAACCAGCAGAAGTGTTCTGGAATCCTTTGTGAGGGACAAACACTGAGAAATCAGAGCCGTGTTCTGGCATCCTATGTAGCGACAAACACTCTGAACCCAGCAGCAGTGTTTTGAATCACGTGAGCGACAAACACTCAGAACCCAAAGCAGTGTTCTGGAATACTTTTTGAGGACAATCATTCAGAACCTTGTAGCTGTGTTTCTGGAATCATATGTGAGGGCCAGCGAACACTTTGAACCCAGCTGCAGTGTTTTTGATTCCCCTGTGAAGGGAAAAACACTCAGGGCAGCAGCAGTGTTCTAGAATCAGCGTAATGGGACTAACATTCAGACCCTCAACGGTAACTTTTGGTCTATGTGAGGGACAAACACTGAGAACCCAACTGCAGTATTCTGCAATCCTTTGTGACAGAGAAACACTCAGACCATCGTAGCAGTGTTCTGGCATCCTATGTGCAGGAAAAACACTCCAAGAAACCAGCATCAGTGCTCTGGATTCCTTTGTGAGGGACAAACAAACAGAACCAGCAGCAGAGTTCTGGAATCCTATGTTGAGGACAAACACTCCAGAACCCATCAGCAGTGGTCAGAAATAATTTGAGGACAAACATTCAGAACCTAGTAGCAGTGTTCTGGAATAGTATGTGAGGACAAACACTCTAGGCAAACTGGCAGTCTTTTGGAATCACACGTGAGGGACAAAAACTCCAGAACCAAGCAGCAATGTTCTGAATACCATGTGAGAGACAACACTCAGAGCCCAGCAGCAGTGTTCTGGAATCTTATTTGAGTGACAAACACTGAGCTTAGCAGCAGAGTATTTACAGAGTCCTTTATGAGAACAAACTTCAGACACGCAGTCTTAAGATCCTATGTGAGAGACAAACCCTCAGAACCTTGAAGCAATGTTCTGCAATCCTTTTTGTTGGACAAACATTCCAGACCCTCGTAGCAGTGTTCCAGAATCCTATGTGGCGAAGGAACAAACACTCAGAACCCAGCAGTAGTGTTCGGGAATCCTATGGGAGGGACAACCATTTCCAGATCCAGCAGCAGTGTTGTGTAGTCTGTGAGGACAAACACTTTCAGAACCCAGCAGCTGTGTTCTGAAACCTATGTGAGGAAAATCATGAACCCAGCGTGTTGTGTTCTGGAATCCTATCTGAGGGAGAAATATTCAAACACTGTAGAAGAGTTCTGGAATCCTATGTGAGGGAAAAACCCTCAGAAGCCAGCAGTGCTCTGGAATCCTTTGAGCAAACAAATCAGAACCCTAGAAGCAGTGTTCTTGGATCTTTCCAGCTAGGAAAAACAGCTTCAAGACCCTCATAATAGTATTTTGGAATCCTATCTGAGGGACAACACTCAGACCAGCAGCTGTGTTCTGGAATCCTATATTATTAAGATAAACACTTAGAACCCAGCACAATATTCTGGAATACTACGTGAGCGACAAACTTTCAGAAGTTTGTAGCAGTATTCTACAGAATTCTATGTGAGGGACAAACACACAAGGCCAACAACTTGATAAGTGGTTCCTAAGTGAGGACAAACATTCAGAACCCAGCAGCAGTGTTCTGGTATCCTATGTGAGGACAAACACTCAGAACCCAGCAGCAGTGTTCTACAGAAATCCCTTTGTGAAGAGAAAAATGGCAGACCCTGCGCAGTGTTCTACTGGAATCCTATGTGATAGAAAAGTTCATACCCTCATAGCAGTGTTCTGGGATCCTATATGAGGTTGGCTTACAGAACCCACCAGCAGCGCTCGGAAACCACACTCTCTAGTGTTCTTGAATCCCATGTGAGAGAAACCTTCATACCCTCGTAGCATTGTTCTGGAATCAATATGAGGACAAACACTCAGAACCAGCCCAACATTCTGGAACCTTTATTGAGGATAAACATTCAGACCGTCATAGCAGTGTGCTGGAATCCTATGTGAGGGACAAATGCTCGAACCCAGCAGCAGTGGACTGGAGTCCTATGTGAGGACAGTACTCTGAGCTTAGCAGCAGTGTTCTGGAATCCTCTGTGAGGGACAAACTTTCACAACTGGCAGTGTTCTGGAGGCTTGTGAGTACAAACATTCAGAACCCAGCAGTGTTCTGGAAGTCCTTTGTGAGAACATTGTTGGAACCTCATAGCAATGTTCAGGGAGTAGGCGTACGTAAGGGACAAACACTCAGGAACACAGCAGCAGTGTTCTGCAATCCCATATGGACAAACACTCGAACCCAGCTGCAATGTTCTGTAATCCCTGTTTGACGACAAAGGCTCAGAAACCAGCAGCACTGTTCAAGAATCCTTTTTTGTGTGACAAACATTCTGAACCTCTAAAAGCAGTGTTCTGGAATCCTACTGTGAGGACAAACACCACAATCCCTGCAGCAGTTTTCTGGAATCCTTTGTGATGGACAAACATATTCAGACCCTCGTAGCAGTTTTCAGAATCCTATGTGTGGGACAAACACTCAGAACACAGCAACAGTGGTCTAGAATCCTTTGTGTGGGACAAAGATTCAGAACCCAGCAGCAGTGTTCTGGAATCCTATCAGGTACAAACACTCAGAAACAGTACAGCTTGTACTTTTGGATTCCACTGTGTACTGGAATCCTATCTGAAGGAAAAACATTCCGAACTTCGTAGAAGTTTTGGAATCCTGTGTGACGGACAAACACTAGAAATCTGCAGCAGTGTTCTAGAATCCTTTCTGAGTGACAAACAAACAGAACCCAGGAGCAGTGTGCTGCTATCCTTTTGAGGAAAAACTTTCACATCCTTATAGCAGTGTTCTGAAACCTATGTGAGGAAAGAAATTCAGACCCTCGTAGCAGTGCTCTGGAATCCTATATGAGGACAAACACTCAGAACCCAGCAGCAGTCTTCTGGAATCCTTTGGAGGAAAAACATTCACACCCTCGTAAAAGTGTTCTGGAATCTGTGAAGGAAAACATTCAGACCCTCGTAGCATTGTTCTGGAATCTAATATGAGGACAAACAGTCAGAACCCAGTTGCAGTGTTCTGGAATACTATGTGAGTGACAACACTCAGAACCCAGGAACTGGGTTCTGGAATTGTCTGTGCGGGCCAGTCATTCAGAACCTCATTATGATATTTCTGAGTCTATGTGAGGGAAAAACACTGTGATCTCAGCAGCAGTGTTCTGGAATCTATGTGAGGGCGAAACCTCTGACCAGCAGTCGTGTTCTGGAATCCCATGTGAGACAAACACTGAGATCTAGCAGCCTGTTCTGAATCCTATGTGAGTACAAACTCTCAGAACCCAGCAGCAGTGTTATGGAGTCCTTTGTGAGAGACAAACATTCAGACCCTCGTAGCAGTGTTCTGGAATCTTGTGAGGCACAAACACTCACAGCAGTAGACCCTCGTAGGAGTGTTCTGGAATCTACGTAAGGGACAAACACTCAGAACTCAGTGATTATTTTCTTGAAAGCTAAGTGAGTACAAACACTCGAAACCAGCAGTGTTCTGGGAATCTTGGTGAGGACTAACACTCCAGAACCCAACAGCATGTTCTGGGAGTATATGTGAAACAAGAACTCAAGAACTCAAACAGTGTTCTGGAATCGTATGTGAGGAACAAGCAATCAGGGCCAGCAGCAGCAGCCATGGAATCCTATGTGAGGGACAAACACTCAAACCCAGCCACTGTGTTCTGGAAACCTATCTAGTGATGACAAACATTCAGACACTCGTGGAAGTGTTCTGGAATCCTCGTGAGAGGCGGCTCAGAAACCAGCATAGGTGTTCTGGAATCCTTTTTGTGGAGAAACAAACAGAACCCAGCAGCAGTCTTCTGGAATCTATGTGAGGGAAAATATTTAGAACCCCGTAGCAGTGAAATACCTGGAATTCTATGAGGACACAACACACAGGACCCAGCAGCAGTGTTCTGGAACCTTATGTGATGGACAAACACTGAGAACACAACAGCAGTGTTCTGAAATCACATGTCAGCAGAAAAACATTCAGAAATTCATAGCAGTGTTCTGGAATCCTTTGTGACAGACAACACTCAGACTGTCGTAGCAGTGTTCTGATTTCCCATGAGAACAAACACAGCTAACATGTCTCAAAATCTCATGGGATCTATGCAAGGAACAACACAAGAGCACCCACACTATGTTCTTAAATACTAAAGAAACAACTTATTCAAACACTGGCCAAAGTATTCTAGAATCTATGTGAGGATAAACACTCAGAAACCAGCAGCAGTATTCTGGAATCCTTTGTGAGGGAAAAACATTAGACTCACGCATTCTTTAAAAATCTCTGTGTGAGGGACAAACCGTCTGAACTGAGCAGCAGTGTTCTGCAATCACTCTTGAGAGACAAACACTCACAGACAGCAGCAGTGTTCTGAAATCTAAATGAGGAACAAACCCTCAGAGACAGCAGCAGTGTTCTGAGTCCTTGTGGGGTACAACATTCAGAACCTCGAAGCAGTGTTCTGGAATCTATTTGAGGACAAACTCACAGAACCCAGCAGCAGTATTCTGGAATCCCAAGTGAGGGACAAACACTCAGAAACCAGCAGCAGTGTGCTGGAATGCTTTGAGGACAACATTCAGACCTTCGAAGCAGTGTTCTGCAATCCTATGTGATTGACAACTCTCAGAACCTAGGAGCAATCTTCTGTAATCTGTTGTGATGGAGAAACATTCGGAACCTCTTCGCCAGTGTTCTGGAATCTAGGTGTGGGAGAAACACTCAGAATCCAGCAGCAATGTTGGAAGTCTCTGTGAGAAAACACTCAAGGCTCAGCAGCGTAGTGTTCTGGAATCCTATGTGACCAGACAAACACTCAGATCACTGCAGCAGGGGGTCTGAAATCCTATGTGAAGGATAAGCACTCAGAACCCAGGAGCAGCGTTCTGGAATCCTTTCTGAGGACAAACATTCAGAACCTCGTAACAGTGTTCTGGAATCTTATGTGAGGACAAACACTCAGAACCCAACTTGGCAGCATTGTTCTGGAATCTTAGATGTGGGACAAACACTCCAGAACCAGGCATTAACAGTTCTGGAGTCCCATGTGAGGACAAACACTCAGAACCCAACAGCAGTATTCTGGAATCCTATGTGAGTGACAAACACTCAGAATCCAGCAGCAGTGTTCTAGAATTCTTTGTGTGGGACAAGCTTCATGCCCTCAAAGCAGTACTCTGGAATCCTATGTGAGGGAGGAACAGTCACAACCCAGCAGCAGTGTTCAGGAATCCTTTGTGACTGGACAAACATTCAGACCGTCGGAGCAGTGTTCTGGAATCTAAGTGAGGACAAACTACTCAGAACCAAGCCACTGTGTTCTGGAATCCTTCTGAGGGACAAATATTCAGACACCGTGAGTGTTCTGGAATCTATGTGAGGACAAACACTCAGAAAACAGCAGCAGTGCTATGGAGACCTTTGTGAGGAGCAGCAAACACAGCCAGAGTTTTATTCTGTAACCTTTTTGAGAGAAAACATTCAGAACCCCGTAGCAGTGTTCTGGAATCTATGTAGGGGACAAACATTCAGAACCCAGCAGCCGTGTTTTGGAATCCTGAGTGAAGACAAAGATTCAGAACTTCATAGCACTGTTCTGGAATCCCAGCTGAGACAGAAACACTCAGAACCCAGCAGTGTTCTAGAATCTATGTGAAGACAAACCCTCAGAACCCAACAGCAGTGTTCTGGAATCCATGTGAGGGACAAACACTCAGTACCCAACCACTGTGTTCTGGAATCCTATATGAAAAGGGACAAACATTCAGACAATCGTAGAAGTGTTCTGGAATCCTATATGAGGACAACACTCAGAAACCACCAGCAGTGCTCTGGAATCTTTTGTGAGGACAAAAATCTGAACCCAGCAGCACTCATTATTCTCTAATCATTTTAGGGACAAACGTTCAGAACCTCGTAGGAGGTTCTTGAATCTAAGTGAGGATAAAGCCCAGGCAGCAGCAGTGTTCTGGAATCTGCGTGAGTGACAAACACTCCGAACCCCGCAGGAATGTTCTTGAATCCTTTGTGAGGGACAAACATTCAAACCCTCGAAGCTATGGTGCTATGGAATCTATACATGAGGTACAAACAGTCATAACCCAGCAGAAATCTTCTGGAATCCTTGTTATGGACAAACATTGAGCCCTTGTAGCAGTGTTACGATCTAATGGAGGCACAAACACTCAGAACCCAGCAGCAGTGTTCTGGAATCTTATGTGAGGGACAAACACTGCAATCCAGCAGAAGTGTTCTGGAATCCTATCTGAGGACATACACTCAGAACCCAGTAGCAGTATTCTGGAATTCTATGTGATGGTACACGCTCAGAAACCAACAGCTGTTTTCTGGAATCTTGTCCAGTGACAAATATTCAGACACTCGTGGAAGTGTTCTGGAATCCTATGTGAGGGATAAACACTCAGAAACTAGCAGCGGTGATCTGGAATCCTTTGTAGAGGCTCAACAGAACCCAGCAGCTGTGTTCTGGAATCTTTGTGAGGAAAAATATTTAGACCCTTGTAGCAGTGTTCTGGAATCTATGTGAGGGACAAACACTGATACAACCCAGCGGCAGTGTTCTGGACTCCTCTATGAAGTCAAACCCTCAGAACCCAGCAGCAGTTTTCTGAAATAAAATGTGAGCAACAAACATTCAGAATTTCGTAGCAGAGTTCTGGAATCCTAGCGAGTGACAAACACTCAGGGAAACCAGCAGCAGTGTTCTAGAATCCTTTCTGTGGGACAAACTTTCAGACGCTCAAAGCAGTGTTCTGGAATCCTATGTGATGGACAAACACTCCGATCCCATCAGCAATGTTCTGCAATCCTTTGTGATGGGCAAACATTCAGACCCTCGTAACAGATTTTGGAATCTAAGTGAGGGACAAACACTCCAGAACCCAGCAGCAAGCAGTGTTCTAGAATCCTATATGAAGAACAAACACTCACAACCCAGCAGCCAGTATTGCTAATCTGTTTGAGGGACAAACACTCCAGAACCCACTCACTGTGTACAGGAATCCTATCTACCATGGGCTAACACATTCAGACCCTCGTAGCAGTGTTCTGGAATCCTATGTGAGGAGAAACTCTAAAAAACCAACAGCAGTGCTCTGGAATCCTTTATGAGGGAAAACATTCAGACCTTTAGCAGTGTTCTGGAATCCTATGTGAGGGAAATATTTTCAGAGCCTCATAGCAATGTTTCTTAATCATATATGAGTGACAAACGCCAGAAACCAGCAGCAGTGTTCTGGAATCCCTTGAGAGGGAAAAACATTTACACCTTCATAACAGTGTTCTGGAATCCTTACTGTGGGAAAAATATTCAGACCCTCGTAACAGTGTTCTGGAATCCTATATGAGGGACAAACACTCAAAACCAGCAGCAGTGTTCTGGAATCTATAGCCAGAGAAGCGTACTCAGAGCTGTACAGTGTTCTGGAGTCTATGGAGTGACAAACTTTTGAAATTCGCTGGCAGTATTCTGGAATCTTATGTGAGGACAAACACACAGAACCCAGTAGCAGTGTTCTGGAATCTTATGTGAGTAACAAACACTCAGAATCCAGCAACAGTGTTCTGGAATCCTATGTGAGGACAAACACTCCAGAACTAGCAGCAGTGTTCTAGGAATACTTTGTGAGGAAAAACACTCAGAACACAGTAGTGTTCTGGTATCCACTATTATTATAGAATCCTATCTGAGACAAACATTCAGAACCTAATAGTAGAAATGTTGCAATTCTACGTGAGGGACAAATACTAAGAAATCTGCAGCAGTGCTCTGGAATCTATTGTGAAGGTCAAACAAATAGAACCCAGTAGCCTTGTTCTACAATACTTTATGAGGAAAAACTTTCAGACCCTCATGGTGGTCTGGAATCACACGTAGGAACAAACACTCAGAGACAGCAGCAGTGTTCTGTACTCCTTTGTGAGGACAACATTCAGTTCCTCAGAGCAGTATTTGGAATCCTATGCTTTGAATGACAAGCACTAAGAAACCATCAACAGTGTTCTGGAATCTATGCTGAATGACAAACCTAAGAAACCATCAGCAGTGTTCTGGAATCCTTTGTGAGTAGCTAAACATTCGACCCCCTTAGCAGGGTTCTGGAACTATGTGAGGACATTCAGACACTTAGCAGTGTTTTGGCGCCTTAGCAGTGTTTGGAAACCAATGTGAGGGCCAAACAGTCAGAACCCAGCATCAGTGTTCTGGAATACTTGGTAAGGGACAAGCATTCAGAAAATCTTATCAGTTTTCTGGAATCCCAACTGAGGAGAAACGCTCCAGAAAATATCTGCAGTGTTCTAGAATTCTATGTGAGGACAAACCCTCATTGCGAGCTGCAGTGTTCTGGATTCCCTAGGTGAGGGACAAACACTCCAGAACAAAGCAGCAGTGTTCACAGTCTCATAACGATGGACAAAAACTCAGAACCCAGCAGTGTTCTGATACCTATGGGAGGGACAAACACTCAGAACCCAGCCCCTGTGTTCTGGAATCCTATCTGAAGGACAAACATTCGGAGACTTGAAGAAGTTTTCTGGAATCTATGTGAAGGACAAACAGTCAGAAACCTGTAGCAATGTTCTGGAATCATTTGCAGGAACAAACACTCAAAACTCAAAAGCAGTATCCTGGAATCCTACGTGAGGCCCAAGCCTAAGAACCCAGCAGCAGTATTTTCGAATCCTTAATGAGTGACAAACAGTCCAGAAACTTGCAACATTATTTTAGGTTGCTGTCTCTAGTACAGAGTTCTGGCCAAGAACAAACGCCAGAACAACCACTGTATTTCACAGAATATTGCTCTGAGAAAAAATAGCCGAGCCTCGTAGAAATTATTTCACAGAATCCCTATGGTAACCAAATACTCGAAAACCGCTCAACAGTGCTCTGGAATCCTTTGTGATGGATAAATAAACAGAGCCCAGCAGCAGTGTTCTGGAATCCTTCGTGAGGACAAACATTCAGAACCTTGTAGCCGTGTTCTGGAATCGTATGTGAAGGGTCAAACACTTTGAACCAGCAGCTGTGTTCTGGAATCTCTATGTGAGGGACAGAAGCACTAGAACCCAGCAACAGTGTTCTGTAATCCTTACTAGTAGAGGACAAAGCACAAGAGCCTTAGCATTGTTCTGCAATCCTTTGTGTGGGGACAAAACACTCAGGCCCAGCAGCAGAGTTGAATCCCATGTGAGGGACAAACGTTCAGGCACTCAGAATAGTGTTTGGAATCCTATGTTAGGGACAAACACTCAGAAAACTGCAGCAGTGTTCTGGAATCACACGTGGGGATGTGACTGAATCCTGATAGCACTGTTGTGGAATGCTCTGTGAGGAACAAACAATCAGACCCTCATCAGCAGTGTTCACAATCCTATGTAAGTACAAACCCTCACAACTCAACTAACTTTCTGGAATTCTATGCGAGGACAAACTCAGAACCTAACAACTTGTTCTGGAATCATACGTAAGGTAATAACACTCAGAACCCTGCAGCAGTGTTCTGGAATGCTATGTAAGAGACAAACACAAAACAGAGCAGTAGTATTCTGGTATCCTATATGAGGTAAAAACACTCAGAGACAACAGAAGTGTTCTGAAATCTATGTCAGGCACAAACATTTAGAGCTCCCAGAAGTGTTCTGGAATATTATGTGAAGGACAAAAACTCAGAATCAGGTGCAGTATTCTGGAATCCTATGTGAGGGACAAACATTCAGACCCTCCTAGCAAGTGTTCTGGAATGCAATCTGTTGTAAAAACCCTCAGAACACAGAAGCAGTTGTCTGGAATCCTTTGTGATGAAGAAACTATTCCAGACCCTAGTAGCAGTGTTCTGGAATCTATGTGACGGACAAACCTTCAGAATCCAGCAATAGTGTACTGGAATCCTCTGTGAGGACATACACTCAGAACCCAGCAGTAGTGTTTTGGAATCCTTTGTGAGGACAAACCCTCAGAATCAGCAGTAGTGTTCTGGAATCCTCTGTGAGGGCCATACCCTCAGAACCAACCCGGTATTGTTCTGGAATCCTATGTCAGGAGGACAAACATTGAAACCAGCAGTTTTCTGGAATCCTATGTGAGGACAAACACTCAGAAACCAGCAGCAGTGTTCTACTGCAATCCCTATGTGAGGACAAACACTCTGGAAACCCAGCAGCAGTGTTCTAGAATCCTATGTGATGACAAACATTCAGAATTTTGTAGCAATGTTCTGCCATTCCATGTGAGTGACAAACACTCAGAAACCAGCAACAGCCTTCTAGAATCTATCGCAAGGAAAAACACTCAGAAGCCAGCAACAATGTTCTAGCATCCCTTGTGAGGGACAAACATTCAGAATCTCGTAGAAGTGCTCTGGAATCGCAAGTGAGGGAGAAACACACAGGCCCAGCAGCCCAATGTTTTGGAATCCTGTTTGAGCGACAAAGATACAGAACTCGTTGCAATGTTCTGGAATCCCATGTGAGGGACAAACACTGTGAGAATCCCAGCAGCAGTGTCTATGAGCTTATTACAGCTTACACATTTTTGTTACCCTTTTGCGCATTTTTATGTGCACACACACCAACCCACCCACCCACTTACACTATGTGAACAAACACTCAGAACCCAGCAGTGTTCTACAATCTATGTGAGGACAAACATTCAAGCTCATGTAGTGTTCTGCAATCCCTGTGTGAGGACAAACACTCAGAACCCAGCCACTGTGTTCTGGAATCTATCTGAGGACAAACATTCAGACACTTGGCAGAAGTGTTCACAGAATCCTATGAGGGTAAACACTCAGAAACAAGCAGCGGTGCTCTGGAGATGCCACAGAGGGACAAACAGAGCCCAGCAGTGTCCTGGAATCGAGGAAAATGGTGAGACCCTCGTCTCAGTTTTTACAATCCTATGTGAGGGAGAAACACTCAGAACTGGCAACAGTGTTCTAGAATCCATGTGAGAGACAAACACTGAGTTCTAGCAGCCCTGTTCTGGAATCCTATGTGAGTACAAACTCAGACACTCACGAAGCAGTGTTTGGGATCCCTATGTGAGGACCGGTCAGAACCTTGGCAGTCTTCTGATTCCCTAGAGTGGCTGTTCCGACCCTCGCTTGAGGATTCTGGAATCTATGTGAGGACAAACGCCAGAACCTACCCCTTAGTATTACAGAATCTTGAACAATACTCAAGGCGCGCAGGGTC',
)
expect(r1.get('cigar')).toEqual(r2.get('cigar'))
expect(r1.get('cigar')).toBe(
'48M4D36M1D97M5D14M1D5M1D37M2D44M1D5M1I11M2I3M2D6M2I8M1D45M3D43M1D4M2D41M1D58M1D31M2D7M1D31M5I3M1D24M2D1M1D19M1D8M1D16M2D25M1I11M1I14M2I7M1D10M2I1M1I4M1I8M1I8M1I18M2D7M1D8M1D64M2D38M1I17M2I13M1I32M2I16M1D11M1D6M1D5M3D41M1I20M1D6M1D47M1I72M4D50M1I71M1I5M3D8M1I25M1I2M1D5M1D4M1I20M1D3M2D10M1I57M1I49M1D34M1I12M2D6M1I5M1I24M1I14M2D11M1I71M1I55M1D48M1D9M2D30M1D100M1D46M1D24M1I49M2D39M3D17M1D41M1I6M1D10M3D8M1I161M2D3M1D12M1D62M1D23M1I12M5D1M2I37M2D12M1D3M1I1M2D68M1I4M1D39M1I13M1D4M2I7M2D14M2I2M1I2M1I16M1D40M1D3M1D25M1D24M1I48M1D17M2D23M2D89M1D8M1D11M2I84M1D14M2D2M2D75M1D49M1I37M1D56M1D38M1D47M1I9M2D2M1D8M1I3M2D30M1D38M1D3M1I16M1D25M1D8M1D28M4D6M1I9M1D47M1D5M3I1M1I26M1D149M1I20M2D7M1I3M1D14M1D4M2I20M2I49M1I9M1D17M3D40M1I1M2D20M1I33M1D39M4D18M2D3M1D2M1D11M2D3M1I8M1I83M1D8M1D18M3D18M1I1M2D9M1I6M1I12M2D29M1D13M3D18M3D53M1D38M2I6M3I6M2D17M1I12M1D1M1D3M2D56M3I1M1D11M2D5M2D24M1D44M2I3M1D6M2I13M1I20M3D19M1D3M3I4M2I26M1D39M1I11M1I32M2D2M1I48M1D54M1D49M1D42M1I5M1D59M2I18M1I9M1D8M1D15M1I14M1I3M1I11M1I14M3D4M1D3M1D11M4D9M1I2M1D18M1I26M1I6M2D86M1I39M1I14M3I95M2D6M2I5M2I3M1D3M1I27M1D47M1D45M3D38M1D48M2D26M1I4M1I24M1D20M1D2M2D13M1D73M2I23M1I1M2D3M1D13M1I12M4D18M2D35M1I10M1D23M2D7M1D77M1D83M1D4M1D3M1D41M1D64M1D25M1D31M1D8M2D27M1D27M1D29M1I22M3I45M1I14M2D23M2I1M3D2M1I22M1D3M1D4M2I5M1D120M2I52M1D42M1I31M2D3M1D47M1D59M1I22M1D18M1D57M2D14M1I3M2I16M1D6M1D6M2D14M2D71M1I35M4I59M1I30M3D5M1D10M2I23M1D13M1D9M2D1M1D7M2I2M1D44M1D46M3D21M2D3M3D6M1I11M1I24M2I4M1D9M2I3M1I40M1D10M2D28M2I83M2I25M2D4M1I9M1D5M2I4M1D11M1D47M1D35M3I3M1I12M1I6M1D10M1I1M3D8M3I23M2D41M2I1M4D26M1D15M4D23M2D37M1D8M1D16M1D4M2I5M3D18M1D59M1D35M1D4M1D61M2D1M2D12M1D5M1D5M1D18M3D16M1I11M5D5M2I23M1I5M3I23M1I32M3D12M1D25M1I9M1D40M1I28M2I23M1I4M1D56M2I19M1D110M2D25M2I4M1D5M3I63M2D27M1D82M1D33M1D13M1D47M1D43M1D3M1D39M3D8M1D44M1D115M3I6M1D1M1D4M1D4M1D47M1D17M1D6M2D28M2D17M1D7M1D8M1D13M1D88M2D20M8D6M80D26M1D31M1I4M1D20M1D12M1D5M3D12M1I5M1D8M1D11M1I15M1D31M1I8M1D2M1D38M1D14M1I62M3I3M1D41M1D10M1I39M1D38M1D11M1D26M3I1M1I12M2D3M1D5M1I92M1I93M3D8M5D8M4D12M39D2M1I6M1D13M1D8M1I6M2D22M3D6M1D3M2I30M1D8M1D59M1D3M2D4M1D4M3D6M3I4M1I69M2D1M1I23M1D24M1I1M2D15M1D6M1D11M1D33M1D8M1D88M2D5M1D4M1D114M1I14M1D41M2D13M2D2M1D19M2I24M1I27M1I69M1D47M1D20M5I39M1I17M1I19M1D104M1D86M1I39M1D8M1D8M1I56M1D4M1D2M1D12M1D8M1D49M1I11M1D68M1D55M1D67M3D17M1D8M1D38M1D55M3I49M1D46M1D26M4I11M1D35M1D10M1D8M1D4M1D9M3D21M1D82M1I1M2I12M1D4M2I45M1D20M1D20M2D2M1D68M1D35M1D49M1D138M1I7M5D37M1D38M1D23M2I123M1D18M2I163M1D5M1D20M1I67M1I5M1I2M2D3M1D20M1I34M3I5M1D3M2I41M1D50M1D16M2D56M1I4M1D24M1D145M1D25M1D4M1I19M5D5M2I14M1D4M1D15M1D9M1I26M1D95M1D11M1I5M1D17M1I31M3D24M1D2M2I16M2D17M3I12M2D111M1D22M3D18M1D19M1I1M2D29M1D30M1D12M3I42M1D5M1I12M1D40M1I11M1D24M2D8M1D13M2I14M1I1M1I10M1D113M1D11M1I36M1D15M1D22M1I21M1I21M1I10M1D23M3D16M1D96M1D53M1D59M1D50M1I29M2D3M18D8M1D11M2I2M8D2M3D8M1D5M2D10M1I4M1I9M1I6M1D9M1D18M2I4M1I6M1I6M3D4M1I16M1I76M1D46M1I40M1I14M1I2M1I4M1D30M2I1M1I2M1I2M1D7M1I3M1D7M1I3M3D23M1I5M1I10M1D16M3D43M1D67M3D3M1I6M1D56M1I10M2D1M1I10M1D22M2D25M1D7M2D16M1D76M2D55M1I1M2D20M1D23M1D50M1D55M1I74M1I4M1I3M1I27M1D56M1D47M1D17M1D50M1I28M2I11M2D5M3D26M1D31M3I7M1I9M1D14M2I33M1D86M1D119M1D9M2I41M1D40M2I7M1I13M1D2M1I3M4I3M73I6M3D18M3D17M1D8M1D12M2D8M1D15M1I9M1D38M1D8M1D20M1I12M1I10M2D4M1D35M1I2M1I2M2D20M3D18M6D1M1D7M1I1M2D22M1D32M1D21M1D23M1D32M1D7M2D10M2I12M1D6M1I10M4D17M2D10M1D6M3D2M1D6M2D2M1I30M1D8M1D10M1D11M46S',
)
expect(r1.id()).toEqual(r2.id())
})
test('pair across chrom', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/pair_across_chr.bam'),
})
await ti.getHeader()
const ret1 = await ti.getRecordsForRange('1', 0, 272213638, {
viewAsPairs: true,
pairAcrossChr: true,
})
expect(ret1.length).toBe(2)
})
test('too few', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/too_few_reads_if_chunk_merging_on.bam'),
})
await ti.getHeader()
const ret1 = await ti.getRecordsForRange('1', 10000, 10600)
expect(ret1.length).toBe(34)
})
test('long read consistent IDs', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/CHM1_pacbio_clip2.bam'),
})
await ti.getHeader()
const ret1 = await ti.getRecordsForRange('chr1', 110114999, 110117499)
const ret2 = await ti.getRecordsForRange('chr1', 110117499, 110119999)
const findfeat = k =>
k.get('name') ===
'm131004_105332_42213_c100572142530000001823103304021442_s1_p0/103296'
const [r1, r2] = [ret1, ret2].map(x => x.find(findfeat))
expect(r1.id()).toEqual(r2.id())
})
test('long read consistent IDs chm1 pacbio', async () => {
const ti = new BamFile({
bamPath: require.resolve('./data/another_chm1_id_difference.bam'),
})
await ti.getHeader()
const ret1 = await ti.getRecordsForRange('chr1', 116473849, 116473874)
const ret2 = await ti.getRecordsForRange('chr1', 116473874, 116473899)
const findfeat = k =>
k.get('name') ===
'm131009_195631_42213_c100579462550000001823095604021430_s1_p0/145814'
const [r1, r2] = [ret1, ret2].map(x => x.find(findfeat))
expect(r1.id()).toEqual(r2.id())
})
xtest('large chunks', async () => {
const ti = new csi({
filehandle: new LocalFile(require.resolve('./data/out.marked.csi')),
})
await ti.parse()
//index 16 == 'chr17'
const ret1 = await ti.blocksForRange(16, 41248671, 41337570)
expect(ret1[0].fetchedSize()).toBe(10893136)
})