@sjcrh/proteinpaint-server 2.16.0 → 2.17.0

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Files changed (21) hide show
  1. package/dataset/clinvar.hg19.js +53 -51
  2. package/dataset/clinvar.hg38.js +60 -58
  3. package/dataset/clinvar.js +49 -55
  4. package/genome/CriGri.js +23 -1853
  5. package/genome/danRer10.js +48 -1108
  6. package/genome/dm3.js +47 -60
  7. package/genome/dm6.js +48 -1916
  8. package/genome/galGal5.js +48 -23522
  9. package/genome/galGal6.js +48 -512
  10. package/genome/hg19.js +210 -304
  11. package/genome/hg38.js +108 -474
  12. package/genome/hg38.test.js +42 -409
  13. package/genome/hgvirus.js +21 -43
  14. package/genome/mm10.js +70 -135
  15. package/genome/mm9.js +82 -118
  16. package/genome/rn6.js +49 -1000
  17. package/package.json +9 -6
  18. package/server.js +1 -1
  19. package/shared/common.js +4 -0
  20. package/src/serverconfig.js +10 -2
  21. package/genome/genome.sql +0 -54
package/genome/dm3.js CHANGED
@@ -1,60 +1,47 @@
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- module.exports={
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- species:'fruit fly',
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- genomefile:'genomes/dm3.gz',
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- genedb:{
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- dbfile:'anno/genes.dm3.db',
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- },
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- tracks:[
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- {
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- __isgene:true, // only for initialization
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- translatecoding:true,
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- file:'anno/refGene.dm3.gz',
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- type:'bedj',
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- name:'RefGene',
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- stackheight:16,
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- stackspace:1,
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- vpad:4,
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- color:'#1D591D',
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- },
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- {
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- __isgene:true, // only for initialization
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- translatecoding:true,
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- file:'anno/ensGene.dm3.gz',
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- type:'bedj',
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- name:'Ensembl genes',
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- stackheight:16,
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- stackspace:1,
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- vpad:4,
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- color:'#004D99'
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- },
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- {
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- "type":"bedj",
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- "name":"RepeatMasker",
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- "stackheight":14,
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- "file":"anno/rmsk.dm3.gz",
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- "onerow":true,
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- categories:{ "LINE":{"color":"#EDCB8C","label":"LINE"},"LTR":{"color":"#E38CED","label":"LTR"},"DNA":{"color":"#8C8EED","label":"DNA transposon"},"simple":{"color":"#8EB88C","label":"Simple repeats"},"low_complexity":{"color":"#ACEBA9","label":"Low complexity"},"satellite":{"color":"#B59A84","label":"Satellite"},"RNA":{"color":"#9DE0E0","label":"RNA repeat"},"other":{"color":"#9BADC2","label":"Other"},"unknown":{"color":"#858585","label":"Unknown"}}
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- }
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- ],
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- defaultcoord:{
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- chr:'chr2L',
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- start:6718954,
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- stop:6723802,
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- },
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-
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- majorchr:`chr2L 23011544
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- chr2LHet 368872
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- chr2R 21146708
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- chr2RHet 3288761
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- chr3L 24543557
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- chr3LHet 2555491
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- chr3R 27905053
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- chr3RHet 2517507
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- chr4 1351857
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- chrU 10049037
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- chrUextra 29004656
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- chrX 22422827
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- chrXHet 204112
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- chrYHet 347038
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- chrM 19517`,
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- }
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+ "use strict";
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.default = {
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+ species: 'fruit fly',
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+ genomefile: 'genomes/dm3.gz',
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+ genedb: {
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+ dbfile: 'anno/genes.dm3.db',
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+ },
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+ tracks: [
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+ {
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+ __isgene: true,
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+ translatecoding: true,
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+ file: 'anno/refGene.dm3.gz',
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+ type: 'bedj',
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+ name: 'RefGene',
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+ stackheight: 16,
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+ stackspace: 1,
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+ vpad: 4,
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+ color: '#1D591D',
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+ },
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+ {
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+ __isgene: true,
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+ translatecoding: true,
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+ file: 'anno/ensGene.dm3.gz',
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+ type: 'bedj',
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+ name: 'Ensembl genes',
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+ stackheight: 16,
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+ stackspace: 1,
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+ vpad: 4,
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+ color: '#004D99'
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+ },
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+ {
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+ "type": "bedj",
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+ "name": "RepeatMasker",
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+ "stackheight": 14,
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+ "file": "anno/rmsk.dm3.gz",
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+ "onerow": true,
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+ categories: { "LINE": { "color": "#EDCB8C", "label": "LINE" }, "LTR": { "color": "#E38CED", "label": "LTR" }, "DNA": { "color": "#8C8EED", "label": "DNA transposon" }, "simple": { "color": "#8EB88C", "label": "Simple repeats" }, "low_complexity": { "color": "#ACEBA9", "label": "Low complexity" }, "satellite": { "color": "#B59A84", "label": "Satellite" }, "RNA": { "color": "#9DE0E0", "label": "RNA repeat" }, "other": { "color": "#9BADC2", "label": "Other" }, "unknown": { "color": "#858585", "label": "Unknown" } }
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+ }
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+ ],
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+ defaultcoord: {
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+ chr: 'chr2L',
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+ start: 6718954,
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+ stop: 6723802,
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+ },
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+ majorchr: "chr2L\t23011544\nchr2LHet\t368872\nchr2R\t21146708\nchr2RHet\t3288761\nchr3L\t24543557\nchr3LHet\t2555491\nchr3R\t27905053\nchr3RHet\t2517507\nchr4\t1351857\nchrU\t10049037\nchrUextra\t29004656\nchrX\t22422827\nchrXHet\t204112\nchrYHet\t347038\nchrM\t19517",
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+ };