@jbrowse/plugin-trix 2.0.1 → 2.1.0

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Files changed (6) hide show
  1. package/package.json +2 -2
  2. package/src/TrixTextSearchAdapter/TrixTextSearchAdapter.test.ts +7 -12
  3. package/src/TrixTextSearchAdapter/test_data/volvox.ix +194 -0
  4. package/src/TrixTextSearchAdapter/test_data/volvox.ixx +1 -0
  5. package/src/TrixTextSearchAdapter/test_data/volvox2_meta.json +1 -0
  6. package/src/TrixTextSearchAdapter/test_data/volvox_meta.json +163 -0
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-trix",
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- "version": "2.0.1",
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+ "version": "2.1.0",
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  "description": "JBrowse 2 trix text search adapter",
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  "keywords": [
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  "jbrowse",
@@ -55,5 +55,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "ed935bf5612af3818abdc8ef52d100d5d81d33a2"
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+ "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
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  }
package/src/TrixTextSearchAdapter/TrixTextSearchAdapter.test.ts CHANGED
@@ -1,28 +1,23 @@
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  import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
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- import path from 'path'
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  import Adapter from './TrixTextSearchAdapter'
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+ import path from 'path'
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  import configSchema from './configSchema'
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  test('adapter can fetch output files', async () => {
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- const rootTemplate = path
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- .join(__dirname, '..', '..', '..', '..', 'test_data', 'volvox', 'trix')
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- .replace(/\\/g, '\\\\')
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-
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- const urlPath = decodeURI(new URL(`file://${rootTemplate}`).href)
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  const args = {
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  type: 'TrixTextSearchAdapter',
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  textSearchAdapterId: 'TrixTextSearchAdapterTest',
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  ixFilePath: {
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- uri: `${urlPath}/volvox.ix`,
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- locationType: 'UriLocation',
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+ localPath: path.resolve(__dirname, `test_data/volvox.ix`),
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+ locationType: 'LocalPathLocation',
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  },
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  ixxFilePath: {
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- uri: `${urlPath}/volvox.ixx`,
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- locationType: 'UriLocation',
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+ localPath: path.resolve(__dirname, `test_data/volvox.ixx`),
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+ locationType: 'LocalPathLocation',
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  },
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  metaFilePath: {
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- uri: `${urlPath}/volvox_meta.json`,
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- locationType: 'UriLocation',
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+ localPath: path.resolve(__dirname, `test_data/volvox_meta.json`),
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+ locationType: 'LocalPathLocation',
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  },
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  }
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  // create adapter
package/src/TrixTextSearchAdapter/test_data/volvox.ix ADDED
@@ -0,0 +1,194 @@
1
+ 1 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],2
2
+ 1000 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
3
+ 2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],1
4
+ 3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],1
5
+ 7-transmembrane ["ctgA%3A17023..17675"|"gff3tabix_genes"|"m08"|"7-transmembrane"],1 ["ctgA%3A18048..18552"|"gff3tabix_genes"|"m07"|"7-transmembrane"],2 ["ctgA%3A37497..40559"|"gff3tabix_genes"|"m15"|"7-transmembrane"],3
6
+ a ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
7
+ agt221.3 ["ctgA%3A7500..8000"|"gff3tabix_genes"|"agt221.3"|"Match4"],1
8
+ agt221.5 ["ctgA%3A1050..1500"|"gff3tabix_genes"|"agt221.5"],1 ["ctgA%3A1050..7300"|"gff3tabix_genes"|"agt221.5"|"Match3"],2 ["ctgA%3A5000..5500"|"gff3tabix_genes"|"agt221.5"],3 ["ctgA%3A7000..7300"|"gff3tabix_genes"|"agt221.5"],4
9
+ agt767.3 ["ctgA%3A8000..9000"|"gff3tabix_genes"|"agt767.3"|"Match6"],1
10
+ agt767.5 ["ctgA%3A1150..1500"|"gff3tabix_genes"|"agt767.5"],1 ["ctgA%3A1150..7200"|"gff3tabix_genes"|"agt767.5"|"Match5"],2 ["ctgA%3A5000..5500"|"gff3tabix_genes"|"agt767.5"],3 ["ctgA%3A7000..7200"|"gff3tabix_genes"|"agt767.5"],4
11
+ agt830.3 ["ctgA%3A5410..5500"|"gff3tabix_genes"|"agt830.3"],1 ["ctgA%3A5410..7503"|"gff3tabix_genes"|"agt830.3"|"Match2"],2 ["ctgA%3A7000..7503"|"gff3tabix_genes"|"agt830.3"],3
12
+ agt830.5 ["ctgA%3A1050..1500"|"gff3tabix_genes"|"agt830.5"],1 ["ctgA%3A1050..3202"|"gff3tabix_genes"|"agt830.5"|"Match1"],2 ["ctgA%3A3000..3202"|"gff3tabix_genes"|"agt830.5"],3
13
+ an ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2
14
+ and ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
15
+ another ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],1 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2
16
+ appear ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
17
+ apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
18
+ apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
19
+ at ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
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+ b101.2 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
21
+ bac ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
22
+ bnd_a ["A%3A2700..2701"|"volvox_sv_test_renamed"|"bnd_A"],1 ["ctgA%3A2700..2701"|"volvox_sv_test"|"bnd_A"],2
23
+ bnd_b ["A%3A34200..34201"|"volvox_sv_test_renamed"|"bnd_B"],1 ["ctgA%3A34200..34201"|"volvox_sv_test"|"bnd_B"],2
24
+ bnd_u ["A%3A23456..23457"|"volvox_sv_test_renamed"|"bnd_U"],1 ["ctgA%3A23456..23457"|"volvox_sv_test"|"bnd_U"],2
25
+ bnd_v ["A%3A21682..21683"|"volvox_sv_test_renamed"|"bnd_V"],1 ["ctgA%3A21682..21683"|"volvox_sv_test"|"bnd_V"],2
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+ bnd_w ["A%3A21681..21682"|"volvox_sv_test_renamed"|"bnd_W"],1 ["ctgA%3A21681..21682"|"volvox_sv_test"|"bnd_W"],2
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+ bnd_x ["A%3A23457..23458"|"volvox_sv_test_renamed"|"bnd_X"],1 ["ctgA%3A23457..23458"|"volvox_sv_test"|"bnd_X"],2
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+ bnd_y ["B%3A1982..1983"|"volvox_sv_test_renamed"|"bnd_Y"],1 ["ctgB%3A1982..1983"|"volvox_sv_test"|"bnd_Y"],2
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+ bnd_z ["B%3A1983..1984"|"volvox_sv_test_renamed"|"bnd_Z"],1 ["ctgB%3A1983..1984"|"volvox_sv_test"|"bnd_Z"],2
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+ both ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
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+ box ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],2
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+ but ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
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+ cds-apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
34
+ cdss ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
35
+ ctga ["ctgA%3A1..50001"|"gff3tabix_genes"|"ctgA"],1
36
+ ctgb ["ctgB%3A1..6079"|"gff3tabix_genes"|"ctgB"],1
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+ dead ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],2
38
+ eden ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],4
39
+ eden.1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1
40
+ eden.2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],1
41
+ eden.3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],1
42
+ end ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
43
+ example ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],3 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],4
44
+ f01 ["ctgA%3A44705..47713"|"gff3tabix_genes"|"f01"],1
45
+ f02 ["ctgA%3A24562..28338"|"gff3tabix_genes"|"f02"],1
46
+ f03 ["ctgA%3A36649..40440"|"gff3tabix_genes"|"f03"],1
47
+ f04 ["ctgA%3A37242..38653"|"gff3tabix_genes"|"f04"],1
48
+ f05 ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 ["ctgB%3A4715..5968"|"gff3tabix_genes"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],2
49
+ f06 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],1 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2
50
+ f07 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2
51
+ f08 ["ctgA%3A13280..16394"|"gff3tabix_genes"|"f08"],1
52
+ f09 ["ctgA%3A36034..38167"|"gff3tabix_genes"|"f09"],1
53
+ f10 ["ctgA%3A15329..15533"|"gff3tabix_genes"|"f10"],1
54
+ f11 ["ctgA%3A46990..48410"|"gff3tabix_genes"|"f11"],1
55
+ f12 ["ctgA%3A49758..50000"|"gff3tabix_genes"|"f12"],1
56
+ f13 ["ctgA%3A19157..22915"|"gff3tabix_genes"|"f13"],1
57
+ f14 ["ctgA%3A23072..23185"|"gff3tabix_genes"|"f14"],1
58
+ f15 ["ctgA%3A22132..24633"|"gff3tabix_genes"|"f15"],1
59
+ fake ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
60
+ fakesnp ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
61
+ fakesnp1 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
62
+ finger ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
63
+ fingerprinted ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
64
+ form ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3
65
+ gene1 ["ctgA%3A1201..1500"|"single_exon_gene"|"gene1"],1
66
+ gene2 ["ctgA%3A1201..3902"|"single_exon_gene"|"gene2"],1
67
+ gene:hga ["ctgA%3A1100..2000"|"gff3tabix_genes"|"Gene%3Ahga"],1
68
+ gene:hgb ["ctgA%3A1600..3000"|"gff3tabix_genes"|"Gene%3Ahgb"],1
69
+ get ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
70
+ helix ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1 ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],2
71
+ hox ["ctgA%3A28332..30033"|"gff3tabix_genes"|"m02"|"HOX"],1
72
+ i ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
73
+ ig-like ["ctgA%3A33325..35791"|"gff3tabix_genes"|"m04"|"Ig-like"],1
74
+ inv134 ["ctgA%3A2700..10000"|"volvox.inv.vcf"|"inv134"],1
75
+ inv135 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv135"],1 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv135"],2
76
+ inv9000 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv9000"],1
77
+ is ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],4 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],5
78
+ kinase ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 ["ctgA%3A11911..15561"|"gff3tabix_genes"|"m11"|"kinase"],2 ["ctgA%3A14731..17239"|"gff3tabix_genes"|"m14"|"kinase"],3 ["ctgA%3A21748..25612"|"gff3tabix_genes"|"m12"|"kinase"],4 ["ctgA%3A46012..48851"|"gff3tabix_genes"|"m09"|"kinase"],5
79
+ length ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
80
+ loop ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1
81
+ m01 ["ctgA%3A48253..48366"|"gff3tabix_genes"|"m01"|"WD40"],1
82
+ m02 ["ctgA%3A28332..30033"|"gff3tabix_genes"|"m02"|"HOX"],1
83
+ m03 ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
84
+ m04 ["ctgA%3A33325..35791"|"gff3tabix_genes"|"m04"|"Ig-like"],1
85
+ m05 ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1
86
+ m06 ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
87
+ m07 ["ctgA%3A18048..18552"|"gff3tabix_genes"|"m07"|"7-transmembrane"],1
88
+ m08 ["ctgA%3A17023..17675"|"gff3tabix_genes"|"m08"|"7-transmembrane"],1
89
+ m09 ["ctgA%3A46012..48851"|"gff3tabix_genes"|"m09"|"kinase"],1
90
+ m10 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],1
91
+ m11 ["ctgA%3A11911..15561"|"gff3tabix_genes"|"m11"|"kinase"],1
92
+ m12 ["ctgA%3A21748..25612"|"gff3tabix_genes"|"m12"|"kinase"],1
93
+ m13 ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1
94
+ m14 ["ctgA%3A14731..17239"|"gff3tabix_genes"|"m14"|"kinase"],1
95
+ m15 ["ctgA%3A37497..40559"|"gff3tabix_genes"|"m15"|"7-transmembrane"],1
96
+ match1 ["ctgA%3A1050..3202"|"gff3tabix_genes"|"agt830.5"|"Match1"],1
97
+ match2 ["ctgA%3A5410..7503"|"gff3tabix_genes"|"agt830.3"|"Match2"],1
98
+ match3 ["ctgA%3A1050..7300"|"gff3tabix_genes"|"agt221.5"|"Match3"],1
99
+ match4 ["ctgA%3A7500..8000"|"gff3tabix_genes"|"agt221.3"|"Match4"],1
100
+ match5 ["ctgA%3A1150..7200"|"gff3tabix_genes"|"agt767.5"|"Match5"],1
101
+ match6 ["ctgA%3A8000..9000"|"gff3tabix_genes"|"agt767.3"|"Match6"],1
102
+ message. ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
103
+ mrna ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
104
+ mrna1 ["ctgA%3A1201..1500"|"single_exon_gene"|"mRNA1"],1
105
+ mrna2 ["ctgA%3A1201..3902"|"single_exon_gene"|"mRNA2"],1
106
+ no ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
107
+ ok! ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],2
108
+ protein ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1
109
+ protein:hga ["ctgA%3A1200..1900"|"gff3tabix_genes"|"Protein%3AHGA"],1
110
+ protein:hgb ["ctgA%3A1800..2900"|"gff3tabix_genes"|"Protein%3AHGB"],1
111
+ reads ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
112
+ remark:hga ["ctgA%3A1000..2000"|"gff3tabix_genes"|"Remark%3Ahga"],1
113
+ repeat ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
114
+ rna-apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
115
+ rs1041740 ["contigA%3A11340..11341"|"volvox_test_vcf"|"rs1041740"],1
116
+ rs10432782 ["contigA%3A7569..7570"|"volvox_test_vcf"|"rs10432782"],1
117
+ rs112989936 ["contigA%3A10684..10685"|"volvox_test_vcf"|"rs112989936"],1
118
+ rs114905802 ["contigA%3A4035..4036"|"volvox_test_vcf"|"rs114905802"],1
119
+ rs11567845 ["contigA%3A8742..8743"|"volvox_test_vcf"|"rs11567845"],1
120
+ rs116260263 ["contigA%3A6834..6835"|"volvox_test_vcf"|"rs116260263"],1
121
+ rs117304270 ["contigA%3A11832..11833"|"volvox_test_vcf"|"rs117304270"],1
122
+ rs117466144 ["contigA%3A11241..11242"|"volvox_test_vcf"|"rs117466144"],1
123
+ rs118132937 ["contigA%3A9136..9137"|"volvox_test_vcf"|"rs118132937"],1
124
+ rs16988404 ["contigA%3A7173..7174"|"volvox_test_vcf"|"rs16988404"],1
125
+ rs17878802 ["contigA%3A5281..5282"|"volvox_test_vcf"|"rs17878802"],1
126
+ rs17878855 ["contigA%3A3105..3106"|"volvox_test_vcf"|"rs17878855"],1
127
+ rs17880044 ["contigA%3A11774..11775"|"volvox_test_vcf"|"rs17880044"],1
128
+ rs17880487 ["contigA%3A12408..12409"|"volvox_test_vcf"|"rs17880487"],1
129
+ rs17880490 ["contigA%3A8077..8078"|"volvox_test_vcf"|"rs17880490"],1
130
+ rs17880795 ["contigA%3A4260..4261"|"volvox_test_vcf"|"rs17880795"],1
131
+ rs17881180 ["contigA%3A3465..3466"|"volvox_test_vcf"|"rs17881180"],1
132
+ rs17881581 ["contigA%3A3171..3172"|"volvox_test_vcf"|"rs17881581"],1
133
+ rs17881732 ["contigA%3A11335..11336"|"volvox_test_vcf"|"rs17881732"],1
134
+ rs17881807 ["contigA%3A5349..5350"|"volvox_test_vcf"|"rs17881807"],1
135
+ rs17882967 ["contigA%3A5006..5007"|"volvox_test_vcf"|"rs17882967"],1
136
+ rs17883234 ["contigA%3A11182..11183"|"volvox_test_vcf"|"rs17883234"],1
137
+ rs17883270 ["contigA%3A5260..5261"|"volvox_test_vcf"|"rs17883270"],1
138
+ rs17883296 ["contigA%3A3000..3001"|"volvox_test_vcf"|"rs17883296"],1
139
+ rs17883461 ["contigA%3A8210..8211"|"volvox_test_vcf"|"rs17883461"],1
140
+ rs17883998 ["contigA%3A9853..9854"|"volvox_test_vcf"|"rs17883998"],1
141
+ rs17884040 ["contigA%3A4248..4249"|"volvox_test_vcf"|"rs17884040"],1
142
+ rs17884233 ["contigA%3A7141..7142"|"volvox_test_vcf"|"rs17884233"],1
143
+ rs17884260 ["contigA%3A4074..4075"|"volvox_test_vcf"|"rs17884260"],1
144
+ rs17884462 ["contigA%3A11689..11690"|"volvox_test_vcf"|"rs17884462"],1
145
+ rs17885219 ["contigA%3A4901..4902"|"volvox_test_vcf"|"rs17885219"],1
146
+ rs17885303 ["contigA%3A9048..9049"|"volvox_test_vcf"|"rs17885303"],1
147
+ rs17885634 ["contigA%3A10252..10253"|"volvox_test_vcf"|"rs17885634"],1
148
+ rs17885833 ["contigA%3A9920..9921"|"volvox_test_vcf"|"rs17885833"],1
149
+ rs17886025 ["contigA%3A8132..8133"|"volvox_test_vcf"|"rs17886025"],1
150
+ rs17886606 ["contigA%3A8328..8329"|"volvox_test_vcf"|"rs17886606"],1
151
+ rs17886692 ["contigA%3A10875..10876"|"volvox_test_vcf"|"rs17886692"],1
152
+ rs2070424 ["contigA%3A10498..10499"|"volvox_test_vcf"|"rs2070424"],1
153
+ rs2234694 ["contigA%3A10043..10044"|"volvox_test_vcf"|"rs2234694"],1
154
+ rs4816405 ["contigA%3A4179..4180"|"volvox_test_vcf"|"rs4816405"],1
155
+ rs4816407 ["contigA%3A11207..11208"|"volvox_test_vcf"|"rs4816407"],1
156
+ rs4817420 ["contigA%3A11549..11550"|"volvox_test_vcf"|"rs4817420"],1
157
+ rs4998557 ["contigA%3A6070..6071"|"volvox_test_vcf"|"rs4998557"],1
158
+ rs6650814 ["contigA%3A4166..4167"|"volvox_test_vcf"|"rs6650814"],1
159
+ rs7277748 ["contigA%3A3152..3153"|"volvox_test_vcf"|"rs7277748"],1
160
+ rs76067554 ["contigA%3A8524..8525"|"volvox_test_vcf"|"rs76067554"],1
161
+ rs76734991 ["contigA%3A11095..11096"|"volvox_test_vcf"|"rs76734991"],1
162
+ rs77112488 ["contigA%3A9884..9885"|"volvox_test_vcf"|"rs77112488"],1
163
+ rs77319474 ["contigA%3A10217..10218"|"volvox_test_vcf"|"rs77319474"],1
164
+ rs78694163 ["contigA%3A8816..8817"|"volvox_test_vcf"|"rs78694163"],1
165
+ rs80265967 ["contigA%3A10781..10782"|"volvox_test_vcf"|"rs80265967"],1
166
+ rs8133032 ["contigA%3A9525..9526"|"volvox_test_vcf"|"rs8133032"],1
167
+ rs9967983 ["contigA%3A8660..8661"|"volvox_test_vcf"|"rs9967983"],1
168
+ seg01 ["ctgA%3A32329..32359"|"gff3tabix_genes"|"seg01"],1
169
+ seg02 ["ctgA%3A26122..26126"|"gff3tabix_genes"|"seg02"],1 ["ctgA%3A26497..26869"|"gff3tabix_genes"|"seg02"],2 ["ctgA%3A27201..27325"|"gff3tabix_genes"|"seg02"],3 ["ctgA%3A27372..27433"|"gff3tabix_genes"|"seg02"],4 ["ctgA%3A27565..27565"|"gff3tabix_genes"|"seg02"],5 ["ctgA%3A27813..28091"|"gff3tabix_genes"|"seg02"],6 ["ctgA%3A28093..28201"|"gff3tabix_genes"|"seg02"],7 ["ctgA%3A28329..28377"|"gff3tabix_genes"|"seg02"],8 ["ctgA%3A28829..29194"|"gff3tabix_genes"|"seg02"],9 ["ctgA%3A29517..29702"|"gff3tabix_genes"|"seg02"],10 ["ctgA%3A29713..30061"|"gff3tabix_genes"|"seg02"],11 ["ctgA%3A30329..30774"|"gff3tabix_genes"|"seg02"],12 ["ctgA%3A30808..31306"|"gff3tabix_genes"|"seg02"],13 ["ctgA%3A31516..31729"|"gff3tabix_genes"|"seg02"],14 ["ctgA%3A31753..32154"|"gff3tabix_genes"|"seg02"],15 ["ctgA%3A32595..32696"|"gff3tabix_genes"|"seg02"],16 ["ctgA%3A32892..32901"|"gff3tabix_genes"|"seg02"],17 ["ctgA%3A33127..33388"|"gff3tabix_genes"|"seg02"],18 ["ctgA%3A33439..33443"|"gff3tabix_genes"|"seg02"],19 ["ctgA%3A33759..34209"|"gff3tabix_genes"|"seg02"],20 ["ctgA%3A34401..34466"|"gff3tabix_genes"|"seg02"],21
170
+ seg03 ["ctgA%3A6885..7241"|"gff3tabix_genes"|"seg03"],1 ["ctgA%3A7410..7737"|"gff3tabix_genes"|"seg03"],2 ["ctgA%3A8055..8080"|"gff3tabix_genes"|"seg03"],3 ["ctgA%3A8306..8999"|"gff3tabix_genes"|"seg03"],4
171
+ seg04 ["ctgA%3A5233..5302"|"gff3tabix_genes"|"seg04"],1 ["ctgA%3A5800..6101"|"gff3tabix_genes"|"seg04"],2 ["ctgA%3A6442..6854"|"gff3tabix_genes"|"seg04"],3 ["ctgA%3A7106..7211"|"gff3tabix_genes"|"seg04"],4 ["ctgA%3A7695..8177"|"gff3tabix_genes"|"seg04"],5 ["ctgA%3A8545..8783"|"gff3tabix_genes"|"seg04"],6 ["ctgA%3A8869..8935"|"gff3tabix_genes"|"seg04"],7 ["ctgA%3A9404..9825"|"gff3tabix_genes"|"seg04"],8
172
+ seg05 ["ctgA%3A26503..26799"|"gff3tabix_genes"|"seg05"],1 ["ctgA%3A27172..27185"|"gff3tabix_genes"|"seg05"],2 ["ctgA%3A27448..27860"|"gff3tabix_genes"|"seg05"],3 ["ctgA%3A27887..28076"|"gff3tabix_genes"|"seg05"],4 ["ctgA%3A28225..28316"|"gff3tabix_genes"|"seg05"],5 ["ctgA%3A28777..29058"|"gff3tabix_genes"|"seg05"],6 ["ctgA%3A29513..29647"|"gff3tabix_genes"|"seg05"],7 ["ctgA%3A30108..30216"|"gff3tabix_genes"|"seg05"],8 ["ctgA%3A30465..30798"|"gff3tabix_genes"|"seg05"],9 ["ctgA%3A31232..31236"|"gff3tabix_genes"|"seg05"],10 ["ctgA%3A31421..31817"|"gff3tabix_genes"|"seg05"],11 ["ctgA%3A32010..32057"|"gff3tabix_genes"|"seg05"],12 ["ctgA%3A32208..32680"|"gff3tabix_genes"|"seg05"],13 ["ctgA%3A33053..33325"|"gff3tabix_genes"|"seg05"],14 ["ctgA%3A33438..33868"|"gff3tabix_genes"|"seg05"],15 ["ctgA%3A34244..34313"|"gff3tabix_genes"|"seg05"],16 ["ctgA%3A34605..34983"|"gff3tabix_genes"|"seg05"],17 ["ctgA%3A35333..35507"|"gff3tabix_genes"|"seg05"],18 ["ctgA%3A35642..35904"|"gff3tabix_genes"|"seg05"],19
173
+ seg06 ["ctgA%3A19249..19559"|"gff3tabix_genes"|"seg06"],1 ["ctgA%3A19975..20260"|"gff3tabix_genes"|"seg06"],2 ["ctgA%3A20379..20491"|"gff3tabix_genes"|"seg06"],3 ["ctgA%3A20533..21005"|"gff3tabix_genes"|"seg06"],4 ["ctgA%3A21122..21331"|"gff3tabix_genes"|"seg06"],5 ["ctgA%3A21682..22176"|"gff3tabix_genes"|"seg06"],6 ["ctgA%3A22374..22570"|"gff3tabix_genes"|"seg06"],7 ["ctgA%3A23025..23427"|"gff3tabix_genes"|"seg06"],8
174
+ seg07 ["ctgA%3A44191..44514"|"gff3tabix_genes"|"seg07"],1 ["ctgA%3A44552..45043"|"gff3tabix_genes"|"seg07"],2 ["ctgA%3A45373..45600"|"gff3tabix_genes"|"seg07"],3 ["ctgA%3A45897..46315"|"gff3tabix_genes"|"seg07"],4 ["ctgA%3A46491..46890"|"gff3tabix_genes"|"seg07"],5 ["ctgA%3A47126..47297"|"gff3tabix_genes"|"seg07"],6 ["ctgA%3A47735..47983"|"gff3tabix_genes"|"seg07"],7 ["ctgA%3A48447..48709"|"gff3tabix_genes"|"seg07"],8 ["ctgA%3A48931..49186"|"gff3tabix_genes"|"seg07"],9 ["ctgA%3A49472..49699"|"gff3tabix_genes"|"seg07"],10 ["ctgA%3A49957..50000"|"gff3tabix_genes"|"seg07"],11 ["ctgA%3A49957..50000"|"gff3tabix_genes"|"seg07"],12
175
+ seg08 ["ctgA%3A18509..18985"|"gff3tabix_genes"|"seg08"],1 ["ctgA%3A18989..19388"|"gff3tabix_genes"|"seg08"],2 ["ctgA%3A19496..19962"|"gff3tabix_genes"|"seg08"],3 ["ctgA%3A20093..20580"|"gff3tabix_genes"|"seg08"],4 ["ctgA%3A20970..21052"|"gff3tabix_genes"|"seg08"],5 ["ctgA%3A21270..21277"|"gff3tabix_genes"|"seg08"],6 ["ctgA%3A21685..22168"|"gff3tabix_genes"|"seg08"],7 ["ctgA%3A22564..22869"|"gff3tabix_genes"|"seg08"],8 ["ctgA%3A22958..23298"|"gff3tabix_genes"|"seg08"],9 ["ctgA%3A23412..23469"|"gff3tabix_genes"|"seg08"],10 ["ctgA%3A23932..23932"|"gff3tabix_genes"|"seg08"],11 ["ctgA%3A24328..24787"|"gff3tabix_genes"|"seg08"],12 ["ctgA%3A25228..25367"|"gff3tabix_genes"|"seg08"],13
176
+ seg09 ["ctgA%3A36616..37057"|"gff3tabix_genes"|"seg09"],1 ["ctgA%3A37208..37227"|"gff3tabix_genes"|"seg09"],2
177
+ seg10 ["ctgA%3A29771..29942"|"gff3tabix_genes"|"seg10"],1 ["ctgA%3A30042..30340"|"gff3tabix_genes"|"seg10"],2 ["ctgA%3A30810..31307"|"gff3tabix_genes"|"seg10"],3 ["ctgA%3A31761..31984"|"gff3tabix_genes"|"seg10"],4 ["ctgA%3A32374..32937"|"gff3tabix_genes"|"seg10"],5
178
+ seg11 ["ctgA%3A24228..24510"|"gff3tabix_genes"|"seg11"],1 ["ctgA%3A24868..25012"|"gff3tabix_genes"|"seg11"],2 ["ctgA%3A25212..25426"|"gff3tabix_genes"|"seg11"],3 ["ctgA%3A25794..25874"|"gff3tabix_genes"|"seg11"],4 ["ctgA%3A26075..26519"|"gff3tabix_genes"|"seg11"],5 ["ctgA%3A26930..26940"|"gff3tabix_genes"|"seg11"],6 ["ctgA%3A26975..27063"|"gff3tabix_genes"|"seg11"],7 ["ctgA%3A27415..27799"|"gff3tabix_genes"|"seg11"],8 ["ctgA%3A27880..27943"|"gff3tabix_genes"|"seg11"],9 ["ctgA%3A28225..28346"|"gff3tabix_genes"|"seg11"],10 ["ctgA%3A28375..28570"|"gff3tabix_genes"|"seg11"],11 ["ctgA%3A28758..29041"|"gff3tabix_genes"|"seg11"],12 ["ctgA%3A29101..29302"|"gff3tabix_genes"|"seg11"],13 ["ctgA%3A29604..29702"|"gff3tabix_genes"|"seg11"],14 ["ctgA%3A29867..29885"|"gff3tabix_genes"|"seg11"],15 ["ctgA%3A30241..30246"|"gff3tabix_genes"|"seg11"],16 ["ctgA%3A30575..30738"|"gff3tabix_genes"|"seg11"],17
179
+ seg12 ["ctgA%3A12531..12895"|"gff3tabix_genes"|"seg12"],1 ["ctgA%3A13122..13449"|"gff3tabix_genes"|"seg12"],2 ["ctgA%3A13452..13745"|"gff3tabix_genes"|"seg12"],3 ["ctgA%3A13908..13965"|"gff3tabix_genes"|"seg12"],4 ["ctgA%3A13998..14488"|"gff3tabix_genes"|"seg12"],5 ["ctgA%3A14564..14899"|"gff3tabix_genes"|"seg12"],6 ["ctgA%3A15185..15276"|"gff3tabix_genes"|"seg12"],7 ["ctgA%3A15639..15736"|"gff3tabix_genes"|"seg12"],8 ["ctgA%3A15745..15870"|"gff3tabix_genes"|"seg12"],9
180
+ seg13 ["ctgA%3A49406..49476"|"gff3tabix_genes"|"seg13"],1 ["ctgA%3A49762..50000"|"gff3tabix_genes"|"seg13"],2
181
+ seg14 ["ctgA%3A41137..41318"|"gff3tabix_genes"|"seg14"],1 ["ctgA%3A41754..41948"|"gff3tabix_genes"|"seg14"],2 ["ctgA%3A42057..42474"|"gff3tabix_genes"|"seg14"],3 ["ctgA%3A42890..43270"|"gff3tabix_genes"|"seg14"],4 ["ctgA%3A43395..43811"|"gff3tabix_genes"|"seg14"],5 ["ctgA%3A44065..44556"|"gff3tabix_genes"|"seg14"],6 ["ctgA%3A44763..45030"|"gff3tabix_genes"|"seg14"],7 ["ctgA%3A45231..45488"|"gff3tabix_genes"|"seg14"],8 ["ctgA%3A45790..46022"|"gff3tabix_genes"|"seg14"],9 ["ctgA%3A46092..46318"|"gff3tabix_genes"|"seg14"],10 ["ctgA%3A46816..46992"|"gff3tabix_genes"|"seg14"],11 ["ctgA%3A47449..47829"|"gff3tabix_genes"|"seg14"],12
182
+ seg15 ["ctgA%3A39265..39361"|"gff3tabix_genes"|"seg15"],1 ["ctgA%3A39753..40034"|"gff3tabix_genes"|"seg15"],2 ["ctgA%3A40515..40954"|"gff3tabix_genes"|"seg15"],3 ["ctgA%3A41252..41365"|"gff3tabix_genes"|"seg15"],4 ["ctgA%3A41492..41504"|"gff3tabix_genes"|"seg15"],5 ["ctgA%3A41941..42377"|"gff3tabix_genes"|"seg15"],6 ["ctgA%3A42748..42954"|"gff3tabix_genes"|"seg15"],7 ["ctgA%3A43401..43897"|"gff3tabix_genes"|"seg15"],8 ["ctgA%3A44043..44113"|"gff3tabix_genes"|"seg15"],9 ["ctgA%3A44399..44888"|"gff3tabix_genes"|"seg15"],10 ["ctgA%3A45281..45375"|"gff3tabix_genes"|"seg15"],11 ["ctgA%3A45711..46041"|"gff3tabix_genes"|"seg15"],12 ["ctgA%3A46425..46564"|"gff3tabix_genes"|"seg15"],13 ["ctgA%3A46738..47087"|"gff3tabix_genes"|"seg15"],14 ["ctgA%3A47329..47595"|"gff3tabix_genes"|"seg15"],15 ["ctgA%3A47858..47979"|"gff3tabix_genes"|"seg15"],16 ["ctgA%3A48169..48453"|"gff3tabix_genes"|"seg15"],17
183
+ should ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
184
+ snp ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
185
+ splice ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3
186
+ sushi ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
187
+ that ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
188
+ the ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
189
+ this ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],4 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],5
190
+ utrs ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
191
+ wd40 ["ctgA%3A48253..48366"|"gff3tabix_genes"|"m01"|"WD40"],1
192
+ with ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],4
193
+ zinc ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
194
+ ああ、この機能は、世界中を旅しています！ ["ctgB%3A4715..5968"|"gff3tabix_genes"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],1
package/src/TrixTextSearchAdapter/test_data/volvox.ixx ADDED
@@ -0,0 +1 @@
1
+ 1 0000000000
package/src/TrixTextSearchAdapter/test_data/volvox_meta.json ADDED
@@ -0,0 +1,163 @@
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+ {
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+ "dateCreated": "2022-06-17T10:57:18.370Z",
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+ "tracks": [
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+ {
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+ "trackId": "volvox_sv_test",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "VcfTabixAdapter",
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+ "vcfGzLocation": {
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+ "uri": "volvox.dup.vcf.gz",
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+ "locationType": "UriLocation"
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+ },
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+ "index": {
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+ "location": {
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+ "uri": "volvox.dup.vcf.gz.tbi",
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+ "locationType": "UriLocation"
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+ }
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+ }
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+ }
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+ },
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+ {
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+ "trackId": "volvox_sv_test_renamed",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "VcfTabixAdapter",
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+ "vcfGzLocation": {
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+ "uri": "volvox.dup.renamed.vcf.gz",
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+ "locationType": "UriLocation"
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+ },
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+ "index": {
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+ "location": {
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+ "uri": "volvox.dup.renamed.vcf.gz.tbi",
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+ "locationType": "UriLocation"
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+ }
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+ }
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+ }
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+ },
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+ {
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+ "trackId": "volvox_test_vcf",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "VcfTabixAdapter",
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+ "vcfGzLocation": {
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+ "uri": "volvox.test.vcf.gz",
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+ "locationType": "UriLocation"
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+ },
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+ "index": {
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+ "location": {
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+ "uri": "volvox.test.vcf.gz.tbi",
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+ "locationType": "UriLocation"
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+ }
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+ }
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+ }
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+ },
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+ {
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+ "trackId": "gff3tabix_genes",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "Gff3TabixAdapter",
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+ "gffGzLocation": {
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+ "uri": "volvox.sort.gff3.gz",
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+ "locationType": "UriLocation"
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+ },
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+ "index": {
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+ "location": {
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+ "uri": "volvox.sort.gff3.gz.tbi",
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+ "locationType": "UriLocation"
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+ }
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+ }
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+ }
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+ },
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+ {
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+ "trackId": "volvox_filtered_vcf",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "VcfTabixAdapter",
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+ "vcfGzLocation": {
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+ "uri": "volvox.filtered.vcf.gz",
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+ "locationType": "UriLocation"
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+ },
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+ "index": {
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+ "location": {
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+ "uri": "volvox.filtered.vcf.gz.tbi",
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+ "locationType": "UriLocation"
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+ }
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+ }
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+ }
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+ },
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+ {
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+ "trackId": "variant_colors",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "VcfTabixAdapter",
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+ "vcfGzLocation": {
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+ "uri": "volvox.filtered.vcf.gz",
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+ "locationType": "UriLocation"
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+ },
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+ "index": {
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+ "location": {
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+ "uri": "volvox.filtered.vcf.gz.tbi",
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+ "locationType": "UriLocation"
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+ }
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+ }
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+ }
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+ },
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+ {
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+ "trackId": "single_exon_gene",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "Gff3TabixAdapter",
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+ "gffGzLocation": {
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+ "uri": "single_exon_gene.sorted.gff.gz",
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+ "locationType": "UriLocation"
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+ },
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+ "index": {
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+ "location": {
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+ "uri": "single_exon_gene.sorted.gff.gz.tbi",
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+ "locationType": "UriLocation"
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+ }
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+ }
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+ }
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+ },
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+ {
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+ "trackId": "volvox.inv.vcf",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "VcfTabixAdapter",
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+ "vcfGzLocation": {
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+ "uri": "volvox.inv.vcf.gz",
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+ "locationType": "UriLocation"
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+ },
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+ "index": {
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+ "location": {
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+ "uri": "volvox.inv.vcf.gz.tbi",
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+ "locationType": "UriLocation"
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+ },
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+ "indexType": "TBI"
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+ }
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+ }
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+ },
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+ {
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+ "trackId": "volvox.filtered.lowercase",
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+ "attributesIndexed": ["Name", "ID", "Note"],
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+ "excludedTypes": ["CDS", "exon"],
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+ "adapterConf": {
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+ "type": "VcfAdapter",
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+ "vcfLocation": {
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+ "uri": "volvox.filtered.lowercase.vcf",
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+ "locationType": "UriLocation"
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+ }
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+ }
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+ }
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+ ],
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+ "assemblyNames": ["volvox"]
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+ }