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Fix CRAM mismatches calculation regression in v2.2.0 (#3342)
* Fix regression on CIGAR/mismatch generation in CRAM files * Small test harness for readfeatures * Make sure mismatches and cigar match between bam and cram * Add test files
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| import PluginManager from '@jbrowse/core/PluginManager' | ||
| import { toArray } from 'rxjs/operators' | ||
| import { LocalFile } from 'generic-filehandle' | ||
| import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache' | ||
|
|
||
| import CramAdapter from './CramAdapter/CramAdapter' | ||
| import BamAdapter from './BamAdapter/BamAdapter' | ||
| import { SequenceAdapter } from './CramAdapter/CramTestAdapters' | ||
|
|
||
| import cramConfigSchema from './CramAdapter/configSchema' | ||
| import bamConfigSchema from './BamAdapter/configSchema' | ||
|
|
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| const pluginManager = new PluginManager() | ||
|
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| const getVolvoxSequenceSubAdapter: getSubAdapterType = async () => { | ||
| return { | ||
| dataAdapter: new SequenceAdapter( | ||
| new LocalFile(require.resolve('../test_data/volvox.fa')), | ||
| ), | ||
| sessionIds: new Set(), | ||
| } | ||
| } | ||
|
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| async function getFeats(f1: string, f2: string) { | ||
| const cramAdapter = new CramAdapter( | ||
| cramConfigSchema.create({ | ||
| cramLocation: { | ||
| localPath: require.resolve(f1), | ||
| }, | ||
| craiLocation: { | ||
| localPath: require.resolve(f1 + '.crai'), | ||
| }, | ||
| }), | ||
| getVolvoxSequenceSubAdapter, | ||
| pluginManager, | ||
| ) | ||
|
|
||
| const bamAdapter = new BamAdapter( | ||
| bamConfigSchema.create({ | ||
| bamLocation: { | ||
| localPath: require.resolve(f2), | ||
| }, | ||
| index: { | ||
| location: { | ||
| localPath: require.resolve(f2 + '.bai'), | ||
| }, | ||
| }, | ||
| }), | ||
| ) | ||
| const query = { | ||
| assemblyName: 'volvox', | ||
| refName: 'ctgA', | ||
| start: 1, | ||
| end: 10200, | ||
| } | ||
| const bamFeatures = bamAdapter.getFeatures(query) | ||
| const cramFeatures = cramAdapter.getFeatures(query) | ||
| const bamFeaturesArray = await bamFeatures.pipe(toArray()).toPromise() | ||
| const cramFeaturesArray = await cramFeatures.pipe(toArray()).toPromise() | ||
| return { bamFeaturesArray, cramFeaturesArray } | ||
| } | ||
|
|
||
| type M = { start: number } | ||
|
|
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| async function cigarCheck(f: string) { | ||
| const { cramFeaturesArray, bamFeaturesArray } = await getFeats( | ||
| `../test_data/${f}.cram`, | ||
| `../test_data/${f}.bam`, | ||
| ) | ||
| const cramMap = Object.fromEntries( | ||
| cramFeaturesArray.map(f => [f.get('name'), f.get('CIGAR')]), | ||
| ) | ||
| const bamMap = Object.fromEntries( | ||
| bamFeaturesArray.map(f => [f.get('name'), f.get('CIGAR')]), | ||
| ) | ||
| expect(bamMap).toEqual(cramMap) | ||
| } | ||
|
|
||
| async function mismatchesCheck(f: string) { | ||
| const { cramFeaturesArray, bamFeaturesArray } = await getFeats( | ||
| `../test_data/${f}.cram`, | ||
| `../test_data/${f}.bam`, | ||
| ) | ||
| const cramMap = Object.fromEntries( | ||
| cramFeaturesArray.map(f => [ | ||
| f.get('name'), | ||
| f.get('mismatches').sort((a: M, b: M) => b.start - a.start), | ||
| ]), | ||
| ) | ||
| const bamMap = Object.fromEntries( | ||
| bamFeaturesArray.map(f => [ | ||
| f.get('name'), | ||
| f.get('mismatches').sort((a: M, b: M) => b.start - a.start), | ||
| ]), | ||
| ) | ||
| expect(bamMap).toEqual(cramMap) | ||
| } | ||
|
|
||
| test('match CIGAR across file types', async () => { | ||
| await cigarCheck('volvox-sorted') | ||
| await cigarCheck('volvox-long-reads.fastq.sorted') | ||
| }) | ||
|
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| test('mismatches same across file types', async () => { | ||
| await mismatchesCheck('volvox-sorted') | ||
| await mismatchesCheck('volvox-long-reads.fastq.sorted') | ||
| }) |
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