@jbrowse/plugin-comparative-adapters 3.6.4 → 3.7.0

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Files changed (7) hide show
  1. package/dist/ChainAdapter/util.js +1 -1
  2. package/dist/DeltaAdapter/util.js +4 -4
  3. package/dist/PAFAdapter/PAFAdapter.js +1 -6
  4. package/esm/ChainAdapter/util.js +1 -1
  5. package/esm/DeltaAdapter/util.js +4 -4
  6. package/esm/PAFAdapter/PAFAdapter.js +1 -6
  7. package/package.json +5 -5
package/dist/ChainAdapter/util.js CHANGED
@@ -62,7 +62,7 @@ function paf_chain2paf(buffer, opts) {
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  const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0;
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  const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
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  if (size_ungapped_alignment !== 0) {
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- num_matches += +size_ungapped_alignment;
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+ num_matches += size_ungapped_alignment;
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  cigar += `${size_ungapped_alignment}M`;
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  }
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  if (diff_in_query !== 0) {
package/dist/DeltaAdapter/util.js CHANGED
@@ -37,10 +37,10 @@ function paf_delta2paf(buffer, opts) {
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  const t3 = +t[3];
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  const t4 = +t[4];
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  strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
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- rs = +Math.min(t0, t1) - 1;
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- re = +Math.max(t1, t0);
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- qs = +Math.min(t2, t3) - 1;
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- qe = +Math.max(t3, t2);
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+ rs = Math.min(t0, t1) - 1;
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+ re = Math.max(t1, t0);
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+ qs = Math.min(t2, t3) - 1;
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+ qe = Math.max(t3, t2);
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  x = y = 0;
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  NM = t4;
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  cigar = [];
package/dist/PAFAdapter/PAFAdapter.js CHANGED
@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  return (mod && mod.__esModule) ? mod : { "default": mod };
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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- const configuration_1 = require("@jbrowse/core/configuration");
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  const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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  const util_1 = require("@jbrowse/core/util");
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  const io_1 = require("@jbrowse/core/util/io");
@@ -62,11 +61,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  getFeatures(query, opts = {}) {
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  return (0, rxjs_1.ObservableCreate)(async (observer) => {
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- let pafRecords = await this.setup(opts);
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- const { config } = opts;
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- if (config && (0, configuration_1.readConfObject)(config, 'colorBy') === 'meanQueryIdentity') {
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- pafRecords = (0, util_3.getWeightedMeans)(pafRecords);
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- }
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+ const pafRecords = (0, util_3.getWeightedMeans)(await this.setup(opts));
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  const assemblyNames = this.getAssemblyNames();
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  const { start: qstart, end: qend, refName: qref, assemblyName } = query;
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  const index = assemblyNames.indexOf(assemblyName);
package/esm/ChainAdapter/util.js CHANGED
@@ -59,7 +59,7 @@ export function paf_chain2paf(buffer, opts) {
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  const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0;
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  const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
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  if (size_ungapped_alignment !== 0) {
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- num_matches += +size_ungapped_alignment;
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+ num_matches += size_ungapped_alignment;
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  cigar += `${size_ungapped_alignment}M`;
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  }
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  if (diff_in_query !== 0) {
package/esm/DeltaAdapter/util.js CHANGED
@@ -34,10 +34,10 @@ export function paf_delta2paf(buffer, opts) {
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  const t3 = +t[3];
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  const t4 = +t[4];
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  strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
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- rs = +Math.min(t0, t1) - 1;
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- re = +Math.max(t1, t0);
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- qs = +Math.min(t2, t3) - 1;
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- qe = +Math.max(t3, t2);
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+ rs = Math.min(t0, t1) - 1;
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+ re = Math.max(t1, t0);
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+ qs = Math.min(t2, t3) - 1;
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+ qe = Math.max(t3, t2);
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  x = y = 0;
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  NM = t4;
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  cigar = [];
package/esm/PAFAdapter/PAFAdapter.js CHANGED
@@ -1,4 +1,3 @@
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- import { readConfObject } from '@jbrowse/core/configuration';
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  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
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  import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
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  import { openLocation } from '@jbrowse/core/util/io';
@@ -57,11 +56,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
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  }
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  getFeatures(query, opts = {}) {
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  return ObservableCreate(async (observer) => {
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- let pafRecords = await this.setup(opts);
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- const { config } = opts;
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- if (config && readConfObject(config, 'colorBy') === 'meanQueryIdentity') {
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- pafRecords = getWeightedMeans(pafRecords);
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- }
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+ const pafRecords = getWeightedMeans(await this.setup(opts));
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  const assemblyNames = this.getAssemblyNames();
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  const { start: qstart, end: qend, refName: qref, assemblyName } = query;
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  const index = assemblyNames.indexOf(assemblyName);
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-comparative-adapters",
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- "version": "3.6.4",
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+ "version": "3.7.0",
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  "description": "JBrowse 2 comparative adapters",
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  "keywords": [
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  "jbrowse",
@@ -38,9 +38,9 @@
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  "dependencies": {
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  "@gmod/bgzf-filehandle": "^4.0.0",
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  "@gmod/tabix": "^3.0.1",
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- "@jbrowse/core": "^3.6.4",
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- "@jbrowse/plugin-alignments": "^3.6.4",
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- "@jbrowse/plugin-linear-genome-view": "^3.6.4",
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+ "@jbrowse/core": "^3.7.0",
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+ "@jbrowse/plugin-alignments": "^3.7.0",
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+ "@jbrowse/plugin-linear-genome-view": "^3.7.0",
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  "@mui/material": "^7.0.0",
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  "generic-filehandle2": "^2.0.1",
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  "mobx": "^6.0.0",
@@ -58,5 +58,5 @@
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  "publishConfig": {
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  "access": "public"
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  },
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- "gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
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+ "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
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  }