jbrowse-plugin-mafviewer 1.1.3 → 1.1.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/MafTabixAdapter/MafTabixAdapter.js +16 -3
- package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -1
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +2 -2
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +3 -3
- package/package.json +1 -1
- package/src/MafTabixAdapter/MafTabixAdapter.ts +14 -3
|
@@ -48,9 +48,22 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
48
48
|
const alns = data.map(elt => elt.split(':')[5]);
|
|
49
49
|
for (const [j, elt] of data.entries()) {
|
|
50
50
|
const ad = elt.split(':');
|
|
51
|
-
const
|
|
52
|
-
const
|
|
53
|
-
|
|
51
|
+
const ag = ad[0].split('.');
|
|
52
|
+
const [n1, n2 = '', ...rest] = ag;
|
|
53
|
+
let org;
|
|
54
|
+
let last = '';
|
|
55
|
+
if (ag.length === 2) {
|
|
56
|
+
org = n1;
|
|
57
|
+
last = n2;
|
|
58
|
+
}
|
|
59
|
+
else if (!Number.isNaN(+n2)) {
|
|
60
|
+
org = `${n1}.${n2}`;
|
|
61
|
+
last = rest.join('.');
|
|
62
|
+
}
|
|
63
|
+
else {
|
|
64
|
+
org = n1;
|
|
65
|
+
last = [n2, ...rest].join('.');
|
|
66
|
+
}
|
|
54
67
|
if (org) {
|
|
55
68
|
alignments[org] = {
|
|
56
69
|
chr: last,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"MafTabixAdapter.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/MafTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAmB,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACnE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAWnC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,sBAAsB;IAC1D,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QAC1B,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC;YACvC,GAAG,WAAW,CAAC,MAAM,CAAC;YACtB,IAAI,EAAE,iBAAiB;SACxB,CAAC,CAAA;QACF,OAAO;YACL,OAAO,EAAE,OAAO,CAAC,WAAqC;SACvD,CAAA;IACH,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa;QACvB,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACtC,MAAM,QAAQ,GAAG,MAAM,cAAc,CACnC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAC3C,CAAA;YAED,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;gBAC/B,MAAM,IAAI,GAAI,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBACzD,MAAM,UAAU,GAAG,EAAoC,CAAA;gBACvD,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBAE/C,KAAK,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,CAAC;oBACtC,MAAM,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBACzB,MAAM,
|
|
1
|
+
{"version":3,"file":"MafTabixAdapter.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/MafTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAmB,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACnE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAWnC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,sBAAsB;IAC1D,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QAC1B,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC;YACvC,GAAG,WAAW,CAAC,MAAM,CAAC;YACtB,IAAI,EAAE,iBAAiB;SACxB,CAAC,CAAA;QACF,OAAO;YACL,OAAO,EAAE,OAAO,CAAC,WAAqC;SACvD,CAAA;IACH,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa;QACvB,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACtC,MAAM,QAAQ,GAAG,MAAM,cAAc,CACnC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAC3C,CAAA;YAED,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;gBAC/B,MAAM,IAAI,GAAI,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBACzD,MAAM,UAAU,GAAG,EAAoC,CAAA;gBACvD,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBAE/C,KAAK,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,CAAC;oBACtC,MAAM,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBACzB,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBAC5B,MAAM,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,CAAC,GAAG,EAAE,CAAA;oBACjC,IAAI,GAAG,CAAA;oBACP,IAAI,IAAI,GAAG,EAAE,CAAA;oBACb,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;wBACpB,GAAG,GAAG,EAAE,CAAA;wBACR,IAAI,GAAG,EAAG,CAAA;oBACZ,CAAC;yBAAM,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,EAAG,CAAC,EAAE,CAAC;wBAC/B,GAAG,GAAG,GAAG,EAAE,IAAI,EAAE,EAAE,CAAA;wBACnB,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;oBACvB,CAAC;yBAAM,CAAC;wBACN,GAAG,GAAG,EAAE,CAAA;wBACR,IAAI,GAAG,CAAC,EAAE,EAAE,GAAG,IAAI,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;oBAChC,CAAC;oBACD,IAAI,GAAG,EAAE,CAAC;wBACR,UAAU,CAAC,GAAG,CAAC,GAAG;4BAChB,GAAG,EAAE,IAAI;4BACT,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;4BACd,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;4BAChB,MAAM,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;4BAC9B,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;4BAChB,IAAI,EAAE,IAAI,CAAC,CAAC,CAAE;yBACf,CAAA;oBACH,CAAC;gBACH,CAAC;gBAED,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;oBAChB,IAAI,EAAE;wBACJ,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;wBAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;wBACvB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;wBAC/B,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC;wBACzB,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;wBAC3B,UAAU;wBACV,GAAG,EAAE,IAAI,CAAC,CAAC,CAAC;qBACb;iBACF,CAAC,CACH,CAAA;YACH,CAAC;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACxC,MAAM,EAAE,GACN,KAAK,CAAC,GAAG,KAAK,gBAAgB;YAC5B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,MAAM,YAAY,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAEhD,2EAA2E;QAC3E,OAAO;QACP,OAAO;YACL,OAAO,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3C,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;SACvC,CAAA;IACH,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}
|