@jbrowse/plugin-sequence 1.6.4 → 1.6.7

package/dist/plugin-sequence.cjs.production.min.js

@@ -1,2 +1,2 @@
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e.abrupt("return",Object.keys(t).map((function(e){return{refName:e,start:0,end:t[e]}})));case 5:return e.next=7,this.twobit.getSequenceSizes();case 7:return r=e.sent,e.abrupt("return",Object.keys(r).map((function(e){return{refName:e,start:0,end:r[e]}})));case 9:case"end":return e.stop()}}),e,this)}))),function(){return t.apply(this,arguments)})},{key:"getFeatures",value:function(e){var t=this,r=e.refName,n=e.start,o=e.end;return g.ObservableCreate(function(){var e=q(re.mark((function e(a){var i,c,u;return re.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,t.twobit.getSequenceSize(r);case 2:return c=void 0!==(i=e.sent)?Math.min(i,o):o,e.next=6,t.twobit.getSequence(r,n,c);case 6:(u=e.sent)&&a.next(new m({id:"".concat(r," ").concat(n,"-").concat(c),data:{refName:r,start:n,end:c,seq:u}})),a.complete();case 9:case"end":return e.stop()}}),e)})));return function(t){return e.apply(this,arguments)}}())}},{key:"freeResources",value:function(){}}]),a}()},ie={__proto__:null,default:function(e){F(o,y.BaseAdapter);var t,r,n=_(o);function o(e,t,r){var a;E(this,o),a=n.call(this,e,t,r);var i=u.readConfObject(e,"chromSizesLocation");if(!i)throw new Error("must provide chromSizesLocation");var c=w.openLocation(i,a.pluginManager);return a.source=c.toString(),a.refSeqs=a.init(c),a}return C(o,[{key:"init",value:(r=q(re.mark((function e(t){var r,n;return re.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,t.readFile("utf8");case 2:if(n={},(r=e.sent).length){e.next=6;break}throw new Error("Could not read file ".concat(t.toString()));case 6:return r.split("\n").forEach((function(e){if(e.length){var t=z(e.split("\t"),2);n[t[0]]=+t[1]}})),e.abrupt("return",n);case 8:case"end":return e.stop()}}),e)}))),function(e){return r.apply(this,arguments)})},{key:"getRegions",value:(t=q(re.mark((function e(){var t;return re.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.refSeqs;case 2:return t=e.sent,e.abrupt("return",Object.keys(t).map((function(e){return{refName:e,start:0,end:t[e]}})));case 4:case"end":return e.stop()}}),e,this)}))),function(){return t.apply(this,arguments)})},{key:"getFeatures",value:function(){throw new Error("sequence not available")}},{key:"getHeader",value:function(){return{}}},{key:"freeResources",value:function(){}}]),o}()},ce=function(e){F(n,y.BaseSequenceAdapter);var t,r=_(n);function n(e,t,o){var a,i;E(this,n),(a=r.call(this,e,t,o)).seqCache=new S({cache:new k({maxSize:200}),fill:(i=q(re.mark((function e(t,r){return re.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.abrupt("return",a.fasta.getSequence(t.refName,t.start,t.end,L(L({},t),{},{signal:r})));case 2:case"end":return e.stop()}}),e)}))),function(e,t){return i.apply(this,arguments)})});var c=u.readConfObject(e,"fastaLocation"),s=u.readConfObject(e,"faiLocation"),l={fasta:w.openLocation(c,a.pluginManager),fai:w.openLocation(s,a.pluginManager)};return a.fasta=new x.IndexedFasta(l),a}return C(n,[{key:"getRefNames",value:function(e){return this.fasta.getSequenceNames(e)}},{key:"getRegions",value:(t=q(re.mark((function e(t){var r;return re.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.fasta.getSequenceSizes(t);case 2:return r=e.sent,e.abrupt("return",Object.keys(r).map((function(e){return{refName:e,start:0,end:r[e]}})));case 4:case"end":return e.stop()}}),e,this)}))),function(e){return t.apply(this,arguments)})},{key:"getFeatures",value:function(e,t){var r=this,n=e.refName,o=e.start,a=e.end;return g.ObservableCreate(function(){var e=q(re.mark((function e(i){var c,u,s,l,f,p,d,h;return re.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,r.fasta.getSequenceSize(n,t);case 2:for(u=void 0!==(c=e.sent)?Math.min(c,a):a,s=[],f=a+(128e3-a%128e3),p=l=o-o%128e3;p<f;p+=128e3)d={refName:n,start:p,end:p+128e3},s.push(r.seqCache.get(JSON.stringify(d),d,null==t?void 0:t.signal));return e.next=11,Promise.all(s);case 11:(h=e.sent.join("").slice(o-l).slice(0,a-o))&&i.next(new m({id:"".concat(n," ").concat(o,"-").concat(u),data:{refName:n,start:o,end:u,seq:h}})),i.complete();case 14:case"end":return e.stop()}}),e)})));return function(t){return e.apply(this,arguments)}}())}},{key:"freeResources",value:function(){}}]),n}(),ue={__proto__:null,default:ce},se={__proto__:null,default:function(e){F(r,ce);var t=_(r);function r(e,n,o){var a;E(this,r),a=t.call(this,e,n,o);var i=u.readConfObject(e,"fastaLocation"),c=u.readConfObject(e,"faiLocation"),s=u.readConfObject(e,"gziLocation");if(!i)throw new Error("must provide fastaLocation");if(!c)throw new Error("must provide faiLocation");if(!s)throw new Error("must provide gziLocation");var l={fasta:w.openLocation(i,a.pluginManager),fai:w.openLocation(c,a.pluginManager),gzi:w.openLocation(s,a.pluginManager)};return a.fasta=new x.BgzipIndexedFasta(l),a}return C(r)}()};exports.default=ee;
 //# sourceMappingURL=plugin-sequence.cjs.production.min.js.map