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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,81 +1,78 @@ | ||
| //@ts-nocheck | ||
| import { LocalFile } from 'generic-filehandle' | ||
| import VirtualOffset from '../src/virtualOffset' | ||
| import CSI from '../src/csi' | ||
|
|
||
| describe('csi index', () => { | ||
| it('loads test.gff3.gz.csi', async () => { | ||
| const ti = new CSI({ | ||
| filehandle: new LocalFile(require.resolve('./data/test.gff3.gz.csi')), | ||
| }) | ||
| const indexData = await ti.parse() | ||
| expect(indexData.columnNumbers.start).toEqual(4) | ||
| expect(indexData.columnNumbers.ref).toEqual(1) | ||
| expect(indexData.columnNumbers.end).toEqual(5) | ||
| // console.log( ti ); | ||
| let blocks = await ti.blocksForRange('1', 1, 4000) | ||
| expect(blocks.length).toEqual(0) | ||
| blocks = await ti.blocksForRange('1', 0, 2000046092) | ||
| expect(blocks.length).toEqual(1) | ||
| expect(blocks[0].minv.blockPosition).toEqual(0) | ||
| expect(blocks[0].minv.dataPosition).toEqual(130) | ||
| // console.log( blocks ); | ||
| test('loads test.gff3.gz.csi', async () => { | ||
| const ti = new CSI({ | ||
| filehandle: new LocalFile(require.resolve('./data/test.gff3.gz.csi')), | ||
| }) | ||
| const indexData = await ti.parse() | ||
| expect(indexData.columnNumbers.start).toEqual(4) | ||
| expect(indexData.columnNumbers.ref).toEqual(1) | ||
| expect(indexData.columnNumbers.end).toEqual(5) | ||
| // console.log( ti ); | ||
| let blocks = await ti.blocksForRange('1', 1, 4000) | ||
| expect(blocks.length).toEqual(0) | ||
| blocks = await ti.blocksForRange('1', 0, 2000046092) | ||
| expect(blocks.length).toEqual(1) | ||
| expect(blocks[0].minv.blockPosition).toEqual(0) | ||
| expect(blocks[0].minv.dataPosition).toEqual(130) | ||
| // console.log( blocks ); | ||
|
|
||
| const metadata = await ti.getMetadata() | ||
| expect(metadata).toEqual({ | ||
| columnNumbers: { end: 5, ref: 1, start: 4 }, | ||
| csi: true, | ||
| csiVersion: 1, | ||
| depth: 6, | ||
| refCount: 2, | ||
| coordinateType: '1-based-closed', | ||
| format: 'generic', | ||
| firstDataLine: new VirtualOffset(0, 130), | ||
| metaChar: '#', | ||
| refIdToName: ['1', 'ctgB'], | ||
| refNameToId: { 1: 0, ctgB: 1 }, | ||
| skipLines: 0, | ||
| maxBlockSize: 1 << 16, | ||
| maxBinNumber: 299593, | ||
| maxRefLength: 4294967296, | ||
| }) | ||
| const metadata = await ti.getMetadata() | ||
| expect(metadata).toEqual({ | ||
| columnNumbers: { end: 5, ref: 1, start: 4 }, | ||
| csi: true, | ||
| csiVersion: 1, | ||
| depth: 6, | ||
| refCount: 2, | ||
| coordinateType: '1-based-closed', | ||
| format: 'generic', | ||
| firstDataLine: new VirtualOffset(0, 130), | ||
| metaChar: '#', | ||
| refIdToName: ['1', 'ctgB'], | ||
| refNameToId: { 1: 0, ctgB: 1 }, | ||
| skipLines: 0, | ||
| maxBlockSize: 1 << 16, | ||
| maxBinNumber: 299593, | ||
| maxRefLength: 4294967296, | ||
| }) | ||
| }) | ||
| test('loads test.vcf.gz.csi', async () => { | ||
| const ti = new CSI({ | ||
| filehandle: new LocalFile(require.resolve('./data/test.vcf.gz.csi')), | ||
| }) | ||
| it('loads test.vcf.gz.csi', async () => { | ||
| const ti = new CSI({ | ||
| filehandle: new LocalFile(require.resolve('./data/test.vcf.gz.csi')), | ||
| }) | ||
| const indexData = await ti.parse() | ||
| expect(indexData.columnNumbers.start).toEqual(2) | ||
| expect(indexData.columnNumbers.ref).toEqual(1) | ||
| expect(indexData.columnNumbers.end).toEqual(0) | ||
| // console.log( ti ); | ||
| let blocks = await ti.blocksForRange('1', 1, 4000) | ||
| expect(blocks.length).toEqual(0) | ||
| blocks = await ti.blocksForRange('1', 0, 2000046092) | ||
| expect(blocks.length).toEqual(1) | ||
| expect(blocks[0].minv.blockPosition).toEqual(0) | ||
| expect(blocks[0].minv.dataPosition).toEqual(2560) | ||
| // console.log( blocks ); | ||
| const indexData = await ti.parse() | ||
| expect(indexData.columnNumbers.start).toEqual(2) | ||
| expect(indexData.columnNumbers.ref).toEqual(1) | ||
| expect(indexData.columnNumbers.end).toEqual(0) | ||
| // console.log( ti ); | ||
| let blocks = await ti.blocksForRange('1', 1, 4000) | ||
| expect(blocks.length).toEqual(0) | ||
| blocks = await ti.blocksForRange('1', 0, 2000046092) | ||
| expect(blocks.length).toEqual(1) | ||
| expect(blocks[0].minv.blockPosition).toEqual(0) | ||
| expect(blocks[0].minv.dataPosition).toEqual(2560) | ||
| // console.log( blocks ); | ||
|
|
||
| expect(await ti.lineCount('1')).toEqual(37) | ||
| expect(await ti.lineCount('1')).toEqual(37) | ||
|
|
||
| const metadata = await ti.getMetadata() | ||
| expect(metadata).toEqual({ | ||
| csi: true, | ||
| csiVersion: 1, | ||
| depth: 6, | ||
| refCount: 1, | ||
| columnNumbers: { end: 0, ref: 1, start: 2 }, | ||
| coordinateType: '1-based-closed', | ||
| format: 'VCF', | ||
| metaChar: '#', | ||
| firstDataLine: new VirtualOffset(0, 2560), | ||
| refIdToName: ['1'], | ||
| refNameToId: { 1: 0 }, | ||
| maxBlockSize: 1 << 16, | ||
| skipLines: 0, | ||
| maxBinNumber: 299593, | ||
| maxRefLength: 4294967296, | ||
| }) | ||
| const metadata = await ti.getMetadata() | ||
| expect(metadata).toEqual({ | ||
| csi: true, | ||
| csiVersion: 1, | ||
| depth: 6, | ||
| refCount: 1, | ||
| columnNumbers: { end: 0, ref: 1, start: 2 }, | ||
| coordinateType: '1-based-closed', | ||
| format: 'VCF', | ||
| metaChar: '#', | ||
| firstDataLine: new VirtualOffset(0, 2560), | ||
| refIdToName: ['1'], | ||
| refNameToId: { 1: 0 }, | ||
| maxBlockSize: 1 << 16, | ||
| skipLines: 0, | ||
| maxBinNumber: 299593, | ||
| maxRefLength: 4294967296, | ||
| }) | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,55 +1,48 @@ | ||
| //@ts-nocheck | ||
| import { LocalFile } from 'generic-filehandle' | ||
| import VirtualOffset from '../src/virtualOffset' | ||
| import TabixIndex from '../src/tbi' | ||
| import TBI from '../src/tbi' | ||
|
|
||
| describe('tbi index', () => { | ||
| it('loads', async () => { | ||
| const ti = new TabixIndex({ | ||
| filehandle: new LocalFile( | ||
| require.resolve('./data/volvox.test.vcf.gz.tbi'), | ||
| ), | ||
| }) | ||
| const indexData = await ti.parse() | ||
| expect(indexData.columnNumbers.start).toEqual(2) | ||
| expect(indexData.columnNumbers.ref).toEqual(1) | ||
| expect(indexData.columnNumbers.end).toEqual(0) | ||
| // console.log( ti ); | ||
| const blocks = await ti.blocksForRange('contigA', 1, 4000) | ||
| expect(blocks.length).toEqual(1) | ||
| expect(blocks[0].minv.blockPosition).toEqual(0) | ||
| expect(blocks[0].minv.dataPosition).toEqual(10431) | ||
| // console.log( blocks ); | ||
|
|
||
| const metadata = await ti.getMetadata() | ||
| expect(metadata).toEqual({ | ||
| columnNumbers: { end: 0, ref: 1, start: 2 }, | ||
| coordinateType: '1-based-closed', | ||
| format: 'VCF', | ||
| metaChar: '#', | ||
| maxBinNumber: 37449, | ||
| firstDataLine: new VirtualOffset(0, 10431), | ||
| refIdToName: ['contigA'], | ||
| refNameToId: { contigA: 0 }, | ||
| maxBlockSize: 1 << 16, | ||
| skipLines: 0, | ||
| maxRefLength: 536870912, | ||
| }) | ||
| console.warn = jest.fn() | ||
| expect(await ti.blocksForRange('contigA', 7334998796, 8104229566)).toEqual( | ||
| [], | ||
| ) | ||
| expect(console.warn).toHaveBeenCalledWith( | ||
| 'querying outside of possible tabix range', | ||
| ) | ||
| test('loads', async () => { | ||
| const ti = new TBI({ | ||
| filehandle: new LocalFile(require.resolve('./data/volvox.test.vcf.gz.tbi')), | ||
| }) | ||
| it('failing tabix', async () => { | ||
| const ti = new TabixIndex({ | ||
| filehandle: new LocalFile( | ||
| require.resolve('./data/failing_tabix.vcf.gz.tbi'), | ||
| ), | ||
| }) | ||
| const indexData = await ti.parse() | ||
| expect(indexData.columnNumbers.start).toEqual(2) | ||
| expect(indexData.columnNumbers.ref).toEqual(1) | ||
| expect(indexData.columnNumbers.end).toEqual(0) | ||
| // console.log( ti ); | ||
| const blocks = await ti.blocksForRange('contigA', 1, 4000) | ||
| expect(blocks.length).toEqual(1) | ||
| expect(blocks[0].minv.blockPosition).toEqual(0) | ||
| expect(blocks[0].minv.dataPosition).toEqual(10431) | ||
| // console.log( blocks ); | ||
|
|
||
| await expect(ti.parse()).rejects.toThrow(/too many bins/) | ||
| const metadata = await ti.getMetadata() | ||
| expect(metadata).toEqual({ | ||
| columnNumbers: { end: 0, ref: 1, start: 2 }, | ||
| coordinateType: '1-based-closed', | ||
| format: 'VCF', | ||
| metaChar: '#', | ||
| maxBinNumber: 37449, | ||
| firstDataLine: new VirtualOffset(0, 10431), | ||
| refIdToName: ['contigA'], | ||
| refNameToId: { contigA: 0 }, | ||
| maxBlockSize: 1 << 16, | ||
| skipLines: 0, | ||
| maxRefLength: 536870912, | ||
| }) | ||
| console.warn = jest.fn() | ||
| expect(await ti.blocksForRange('contigA', 7334998796, 8104229566)).toEqual([]) | ||
| expect(console.warn).toHaveBeenCalledWith( | ||
| 'querying outside of possible tabix range', | ||
| ) | ||
| }) | ||
| test('failing tabix', async () => { | ||
| const ti = new TBI({ | ||
| filehandle: new LocalFile( | ||
| require.resolve('./data/failing_tabix.vcf.gz.tbi'), | ||
| ), | ||
| }) | ||
|
|
||
| await expect(ti.parse()).rejects.toThrow(/too many bins/) | ||
| }) |
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