@jbrowse/plugin-comparative-adapters 3.0.5 → 3.2.0
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/ChainAdapter/configSchema.js +14 -1
- package/dist/ChainAdapter/util.js +2 -1
- package/dist/DeltaAdapter/configSchema.js +14 -1
- package/dist/DeltaAdapter/util.js +2 -1
- package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js +2 -2
- package/dist/MCScanAnchorsAdapter/configSchema.js +22 -1
- package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js +2 -2
- package/dist/MCScanSimpleAnchorsAdapter/configSchema.js +22 -1
- package/dist/MashMapAdapter/configSchema.js +14 -1
- package/dist/PAFAdapter/configSchema.js +14 -1
- package/dist/PairwiseIndexedPAFAdapter/configSchema.js +20 -1
- package/dist/util.js +1 -1
- package/esm/ChainAdapter/configSchema.js +14 -1
- package/esm/ChainAdapter/util.js +2 -1
- package/esm/DeltaAdapter/configSchema.js +14 -1
- package/esm/DeltaAdapter/util.js +2 -1
- package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js +2 -2
- package/esm/MCScanAnchorsAdapter/configSchema.js +22 -1
- package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js +2 -2
- package/esm/MCScanSimpleAnchorsAdapter/configSchema.js +22 -1
- package/esm/MashMapAdapter/configSchema.js +14 -1
- package/esm/PAFAdapter/configSchema.js +14 -1
- package/esm/PairwiseIndexedPAFAdapter/configSchema.js +20 -1
- package/esm/util.js +2 -2
- package/package.json +5 -5
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@@ -22,5 +22,18 @@ const ChainAdapter = (0, configuration_1.ConfigurationSchema)('ChainAdapter', {
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type: 'fileLocation',
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defaultValue: { uri: '/path/to/file.chain', locationType: 'UriLocation' },
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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chainLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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exports.default = ChainAdapter;
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@@ -1,6 +1,7 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.paf_chain2paf = paf_chain2paf;
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const util_1 = require("@jbrowse/core/util");
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function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, cigar, numMatches) {
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return {
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qname,
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@@ -36,7 +37,7 @@ function paf_chain2paf(buffer, opts) {
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const decoder = new TextDecoder('utf8');
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while (blockStart < buffer.length) {
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if (i++ % 10000 === 0) {
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statusCallback(`Loading ${
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statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
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}
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const n = buffer.indexOf(10, blockStart);
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if (n === -1) {
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@@ -25,5 +25,18 @@ const DeltaAdapter = (0, configuration_1.ConfigurationSchema)('DeltaAdapter', {
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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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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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deltaLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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exports.default = DeltaAdapter;
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@@ -1,6 +1,7 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.paf_delta2paf = paf_delta2paf;
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const util_1 = require("@jbrowse/core/util");
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function paf_delta2paf(buffer, opts) {
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const { statusCallback = () => { } } = opts || {};
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let rname = '';
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@@ -23,7 +24,7 @@ function paf_delta2paf(buffer, opts) {
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const decoder = new TextDecoder('utf8');
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while (blockStart < buffer.length) {
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if (j++ % 10000 === 0) {
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statusCallback(`Loading ${
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statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
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}
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const n = buffer.indexOf(10, blockStart);
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if (n === -1) {
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@@ -69,7 +69,7 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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const index = assemblyNames.indexOf(region.assemblyName);
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if (index !== -1) {
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const flip = index === 0;
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-
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for (const f of feats) {
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const [r1, r2, score, rowNum] = f;
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const [f1, f2] = !flip ? [r2, r1] : [r1, r2];
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if (f1.refName === region.refName &&
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@@ -87,7 +87,7 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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},
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}));
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}
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-
}
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}
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}
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observer.complete();
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});
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@@ -28,5 +28,26 @@ const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnc
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type: 'stringArray',
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defaultValue: [],
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri && snap.bed1 && snap.bed2
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? {
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...snap,
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mcscanAnchorsLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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bed1Location: {
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uri: snap.bed1,
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baseUri: snap.baseUri,
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},
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bed2Location: {
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uri: snap.bed2,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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exports.default = MCScanAnchorsAdapter;
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const index = assemblyNames.indexOf(region.assemblyName);
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if (index !== -1) {
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const flip = index === 0;
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for (const f of feats) {
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const [f11, f12, f21, f22, score, strand, rowNum] = f;
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let r1 = {
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refName: f11.refName,
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},
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}));
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}
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}
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}
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}
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observer.complete();
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});
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type: 'stringArray',
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defaultValue: [],
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri && snap.bed1 && snap.bed2
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? {
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...snap,
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mcscanSimpleAnchorsLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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bed1Location: {
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uri: snap.bed1,
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baseUri: snap.baseUri,
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},
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bed2Location: {
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uri: snap.bed2,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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exports.default = MCScanSimpleAnchorsAdapter;
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locationType: 'UriLocation',
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},
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},
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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outLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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});
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exports.default = MashMapAdapter;
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locationType: 'UriLocation',
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},
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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pafLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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});
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exports.default = PAFAdapter;
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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pifGzLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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index: {
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location: {
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uri: `${snap.uri}.tbi`,
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baseUri: snap.baseUri,
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},
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},
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});
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exports.default = PairwiseIndexedPAFAdapter;
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package/dist/util.js
CHANGED
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statusCallback(`Loading ${
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statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
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type: 'fileLocation',
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defaultValue: { uri: '/path/to/file.chain', locationType: 'UriLocation' },
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},
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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chainLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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: snap;
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});
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export default ChainAdapter;
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package/esm/ChainAdapter/util.js
CHANGED
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import { getProgressDisplayStr } from '@jbrowse/core/util';
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function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, cigar, numMatches) {
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return {
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while (blockStart < buffer.length) {
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statusCallback(`Loading ${
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statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
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}
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const n = buffer.indexOf(10, blockStart);
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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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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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deltaLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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export default DeltaAdapter;
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package/esm/DeltaAdapter/util.js
CHANGED
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import { getProgressDisplayStr } from '@jbrowse/core/util';
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export function paf_delta2paf(buffer, opts) {
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const { statusCallback = () => { } } = opts || {};
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let rname = '';
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@@ -20,7 +21,7 @@ export function paf_delta2paf(buffer, opts) {
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const decoder = new TextDecoder('utf8');
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while (blockStart < buffer.length) {
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if (j++ % 10000 === 0) {
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statusCallback(`Loading ${
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statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
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}
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const n = buffer.indexOf(10, blockStart);
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if (n === -1) {
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@@ -67,7 +67,7 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
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const index = assemblyNames.indexOf(region.assemblyName);
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if (index !== -1) {
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const flip = index === 0;
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for (const f of feats) {
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const [r1, r2, score, rowNum] = f;
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const [f1, f2] = !flip ? [r2, r1] : [r1, r2];
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73
73
|
if (f1.refName === region.refName &&
|
|
@@ -85,7 +85,7 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
|
|
|
85
85
|
},
|
|
86
86
|
}));
|
|
87
87
|
}
|
|
88
|
-
}
|
|
88
|
+
}
|
|
89
89
|
}
|
|
90
90
|
observer.complete();
|
|
91
91
|
});
|
|
@@ -26,5 +26,26 @@ const MCScanAnchorsAdapter = ConfigurationSchema('MCScanAnchorsAdapter', {
|
|
|
26
26
|
type: 'stringArray',
|
|
27
27
|
defaultValue: [],
|
|
28
28
|
},
|
|
29
|
-
}, {
|
|
29
|
+
}, {
|
|
30
|
+
explicitlyTyped: true,
|
|
31
|
+
preProcessSnapshot: snap => {
|
|
32
|
+
return snap.uri && snap.bed1 && snap.bed2
|
|
33
|
+
? {
|
|
34
|
+
...snap,
|
|
35
|
+
mcscanAnchorsLocation: {
|
|
36
|
+
uri: snap.uri,
|
|
37
|
+
baseUri: snap.baseUri,
|
|
38
|
+
},
|
|
39
|
+
bed1Location: {
|
|
40
|
+
uri: snap.bed1,
|
|
41
|
+
baseUri: snap.baseUri,
|
|
42
|
+
},
|
|
43
|
+
bed2Location: {
|
|
44
|
+
uri: snap.bed2,
|
|
45
|
+
baseUri: snap.baseUri,
|
|
46
|
+
},
|
|
47
|
+
}
|
|
48
|
+
: snap;
|
|
49
|
+
},
|
|
50
|
+
});
|
|
30
51
|
export default MCScanAnchorsAdapter;
|
|
@@ -85,7 +85,7 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
|
|
|
85
85
|
const index = assemblyNames.indexOf(region.assemblyName);
|
|
86
86
|
if (index !== -1) {
|
|
87
87
|
const flip = index === 0;
|
|
88
|
-
|
|
88
|
+
for (const f of feats) {
|
|
89
89
|
const [f11, f12, f21, f22, score, strand, rowNum] = f;
|
|
90
90
|
let r1 = {
|
|
91
91
|
refName: f11.refName,
|
|
@@ -116,7 +116,7 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
|
|
|
116
116
|
},
|
|
117
117
|
}));
|
|
118
118
|
}
|
|
119
|
-
}
|
|
119
|
+
}
|
|
120
120
|
}
|
|
121
121
|
observer.complete();
|
|
122
122
|
});
|
|
@@ -26,5 +26,26 @@ const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapt
|
|
|
26
26
|
type: 'stringArray',
|
|
27
27
|
defaultValue: [],
|
|
28
28
|
},
|
|
29
|
-
}, {
|
|
29
|
+
}, {
|
|
30
|
+
explicitlyTyped: true,
|
|
31
|
+
preProcessSnapshot: snap => {
|
|
32
|
+
return snap.uri && snap.bed1 && snap.bed2
|
|
33
|
+
? {
|
|
34
|
+
...snap,
|
|
35
|
+
mcscanSimpleAnchorsLocation: {
|
|
36
|
+
uri: snap.uri,
|
|
37
|
+
baseUri: snap.baseUri,
|
|
38
|
+
},
|
|
39
|
+
bed1Location: {
|
|
40
|
+
uri: snap.bed1,
|
|
41
|
+
baseUri: snap.baseUri,
|
|
42
|
+
},
|
|
43
|
+
bed2Location: {
|
|
44
|
+
uri: snap.bed2,
|
|
45
|
+
baseUri: snap.baseUri,
|
|
46
|
+
},
|
|
47
|
+
}
|
|
48
|
+
: snap;
|
|
49
|
+
},
|
|
50
|
+
});
|
|
30
51
|
export default MCScanSimpleAnchorsAdapter;
|
|
@@ -23,5 +23,18 @@ const MashMapAdapter = ConfigurationSchema('MashMapAdapter', {
|
|
|
23
23
|
locationType: 'UriLocation',
|
|
24
24
|
},
|
|
25
25
|
},
|
|
26
|
-
}, {
|
|
26
|
+
}, {
|
|
27
|
+
explicitlyTyped: true,
|
|
28
|
+
preProcessSnapshot: snap => {
|
|
29
|
+
return snap.uri
|
|
30
|
+
? {
|
|
31
|
+
...snap,
|
|
32
|
+
outLocation: {
|
|
33
|
+
uri: snap.uri,
|
|
34
|
+
baseUri: snap.baseUri,
|
|
35
|
+
},
|
|
36
|
+
}
|
|
37
|
+
: snap;
|
|
38
|
+
},
|
|
39
|
+
});
|
|
27
40
|
export default MashMapAdapter;
|
|
@@ -23,5 +23,18 @@ const PAFAdapter = ConfigurationSchema('PAFAdapter', {
|
|
|
23
23
|
locationType: 'UriLocation',
|
|
24
24
|
},
|
|
25
25
|
},
|
|
26
|
-
}, {
|
|
26
|
+
}, {
|
|
27
|
+
explicitlyTyped: true,
|
|
28
|
+
preProcessSnapshot: snap => {
|
|
29
|
+
return snap.uri
|
|
30
|
+
? {
|
|
31
|
+
...snap,
|
|
32
|
+
pafLocation: {
|
|
33
|
+
uri: snap.uri,
|
|
34
|
+
baseUri: snap.baseUri,
|
|
35
|
+
},
|
|
36
|
+
}
|
|
37
|
+
: snap;
|
|
38
|
+
},
|
|
39
|
+
});
|
|
27
40
|
export default PAFAdapter;
|
|
@@ -39,5 +39,24 @@ const PairwiseIndexedPAFAdapter = ConfigurationSchema('PairwiseIndexedPAFAdapter
|
|
|
39
39
|
},
|
|
40
40
|
},
|
|
41
41
|
}),
|
|
42
|
-
}, {
|
|
42
|
+
}, {
|
|
43
|
+
explicitlyTyped: true,
|
|
44
|
+
preProcessSnapshot: snap => {
|
|
45
|
+
return snap.uri
|
|
46
|
+
? {
|
|
47
|
+
...snap,
|
|
48
|
+
pifGzLocation: {
|
|
49
|
+
uri: snap.uri,
|
|
50
|
+
baseUri: snap.baseUri,
|
|
51
|
+
},
|
|
52
|
+
index: {
|
|
53
|
+
location: {
|
|
54
|
+
uri: `${snap.uri}.tbi`,
|
|
55
|
+
baseUri: snap.baseUri,
|
|
56
|
+
},
|
|
57
|
+
},
|
|
58
|
+
}
|
|
59
|
+
: snap;
|
|
60
|
+
},
|
|
61
|
+
});
|
|
43
62
|
export default PairwiseIndexedPAFAdapter;
|
package/esm/util.js
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
|
|
1
|
+
import { fetchAndMaybeUnzipText, getProgressDisplayStr, } from '@jbrowse/core/util';
|
|
2
2
|
export function parseBed(text) {
|
|
3
3
|
return new Map(text
|
|
4
4
|
.split(/\n|\r\n|\r/)
|
|
@@ -44,7 +44,7 @@ export function parseLineByLine(buffer, cb, opts) {
|
|
|
44
44
|
}
|
|
45
45
|
}
|
|
46
46
|
if (i++ % 10000 === 0) {
|
|
47
|
-
statusCallback(`Loading ${
|
|
47
|
+
statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
|
|
48
48
|
}
|
|
49
49
|
blockStart = n + 1;
|
|
50
50
|
}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-comparative-adapters",
|
|
3
|
-
"version": "3.0
|
|
3
|
+
"version": "3.2.0",
|
|
4
4
|
"description": "JBrowse 2 comparative adapters",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -38,9 +38,9 @@
|
|
|
38
38
|
"dependencies": {
|
|
39
39
|
"@gmod/bgzf-filehandle": "^2.0.1",
|
|
40
40
|
"@gmod/tabix": "^2.0.0",
|
|
41
|
-
"@jbrowse/core": "^3.0
|
|
42
|
-
"@jbrowse/plugin-alignments": "^3.0
|
|
43
|
-
"@jbrowse/plugin-linear-genome-view": "^3.0
|
|
41
|
+
"@jbrowse/core": "^3.2.0",
|
|
42
|
+
"@jbrowse/plugin-alignments": "^3.2.0",
|
|
43
|
+
"@jbrowse/plugin-linear-genome-view": "^3.2.0",
|
|
44
44
|
"@mui/material": "^6.0.0",
|
|
45
45
|
"generic-filehandle2": "^1.0.0",
|
|
46
46
|
"mobx": "^6.0.0",
|
|
@@ -58,5 +58,5 @@
|
|
|
58
58
|
"publishConfig": {
|
|
59
59
|
"access": "public"
|
|
60
60
|
},
|
|
61
|
-
"gitHead": "
|
|
61
|
+
"gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
|
|
62
62
|
}
|