@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/src/PileupRenderer/components/PileupRendering.tsx

@@ -1,8 +1,8 @@
+import React, { useRef, useState, useEffect } from 'react'
 import { Region } from '@jbrowse/core/util/types'
 import { PrerenderedCanvas } from '@jbrowse/core/ui'
 import { bpSpanPx } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
-import React, { MouseEvent, useRef, useState, useEffect } from 'react'
 import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view'
 
 // used so that user can click-away-from-feature below the laid out features
@@ -91,46 +91,46 @@ function PileupRendering(props: {
     contextMenuFeature,
   ])
 
-  function onMouseDown(event: MouseEvent) {
+  function onMouseDown(event: React.MouseEvent) {
     setMouseIsDown(true)
     setMovedDuringLastMouseDown(false)
     callMouseHandler('MouseDown', event)
   }
 
-  function onMouseEnter(event: MouseEvent) {
+  function onMouseEnter(event: React.MouseEvent) {
     callMouseHandler('MouseEnter', event)
   }
 
-  function onMouseOut(event: MouseEvent) {
+  function onMouseOut(event: React.MouseEvent) {
     callMouseHandler('MouseOut', event)
     callMouseHandler('MouseLeave', event)
   }
 
-  function onMouseOver(event: MouseEvent) {
+  function onMouseOver(event: React.MouseEvent) {
     callMouseHandler('MouseOver', event)
   }
 
-  function onMouseUp(event: MouseEvent) {
+  function onMouseUp(event: React.MouseEvent) {
     setMouseIsDown(false)
     callMouseHandler('MouseUp', event)
   }
 
-  function onClick(event: MouseEvent) {
+  function onClick(event: React.MouseEvent) {
     if (!movedDuringLastMouseDown) {
       callMouseHandler('Click', event)
     }
   }
 
-  function onMouseLeave(event: MouseEvent) {
+  function onMouseLeave(event: React.MouseEvent) {
     callMouseHandler('MouseOut', event)
     callMouseHandler('MouseLeave', event)
   }
 
-  function onContextMenu(event: MouseEvent) {
+  function onContextMenu(event: React.MouseEvent) {
     callMouseHandler('ContextMenu', event)
   }
 
-  function mouseMove(event: MouseEvent) {
+  function mouseMove(event: React.MouseEvent) {
     if (mouseIsDown) {
       setMovedDuringLastMouseDown(true)
     }
@@ -158,7 +158,7 @@ function PileupRendering(props: {
     }
   }
 
-  function callMouseHandler(handlerName: string, event: MouseEvent) {
+  function callMouseHandler(handlerName: string, event: React.MouseEvent) {
     // @ts-ignore
     // eslint-disable-next-line react/destructuring-assignment
     const featureHandler = props[`onFeature${handlerName}`]

package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts

@@ -166,7 +166,9 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
         : undefined
 
     const bins = [] as {
+      refbase?: string
       total: number
+      all: number
       ref: number
       '-1': 0
       '0': 0
@@ -189,6 +191,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
           if (bins[i] === undefined) {
             bins[i] = {
               total: 0,
+              all: 0,
               ref: 0,
               '-1': 0,
               '0': 0,
@@ -201,6 +204,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
           }
           if (j !== fend) {
             bins[i].total++
+            bins[i].all++
             bins[i].ref++
             bins[i][fstrand]++
           }
@@ -318,6 +322,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
               bin.total--
             } else if (!interbase && colorSNPs) {
               inc(bin, fstrand, 'cov', base)
+              bin.refbase = mismatch.altbase
             }
           }
         }

package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts

@@ -39,7 +39,7 @@ interface SNPInfo {
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
   // note: the snps are drawn on linear scale even if the data is drawn in log
   // scape hence the two different scales being used
-  draw(
+  async draw(
     ctx: CanvasRenderingContext2D,
     props: RenderArgsDeserializedWithFeatures,
   ) {
@@ -94,11 +94,13 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     const indicatorToHeight = (n: number) =>
       indicatorToY(getOrigin('linear')) - indicatorToY(n)
 
+    // @ts-ignore
+    const { bases } = theme.palette
     const colorForBase: { [key: string]: string } = {
-      A: theme.palette.bases.A.main,
-      C: theme.palette.bases.C.main,
-      G: theme.palette.bases.G.main,
-      T: theme.palette.bases.T.main,
+      A: bases.A.main,
+      C: bases.C.main,
+      G: bases.G.main,
+      T: bases.T.main,
       total: 'lightgrey',
       insertion: 'purple',
       softclip: 'blue',

package/dist/AlignmentsFeatureDetail/index.test.js

@@ -1,60 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _react = require("@testing-library/react");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _react2 = _interopRequireDefault(require("react"));
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _ = require(".");
-
-var _AlignmentsFeatureDetail = _interopRequireDefault(require("./AlignmentsFeatureDetail"));
-
-test('open up a widget', function () {
-  console.warn = jest.fn();
-  var pluginManager = new _PluginManager.default([]);
-
-  var Session = _mobxStateTree.types.model({
-    pluginManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
-    rpcManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
-    configuration: (0, _configuration.ConfigurationSchema)('test', {}),
-    widget: (0, _.stateModelFactory)(pluginManager)
-  });
-
-  var session = Session.create({
-    widget: {
-      type: 'AlignmentsFeatureWidget'
-    }
-  });
-  session.widget.setFeatureData({
-    seq: 'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG',
-    start: 2,
-    end: 102,
-    strand: 1,
-    score: 37,
-    qual: '17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17',
-    MQ: 37,
-    CIGAR: '100M',
-    length_on_ref: 100,
-    template_length: 0,
-    seq_length: 100,
-    name: 'ctgA_3_555_0:0:0_2:0:0_102d',
-    refName: 'ctgA',
-    type: 'match'
-  });
-
-  var _render = (0, _react.render)( /*#__PURE__*/_react2.default.createElement(_AlignmentsFeatureDetail.default, {
-    model: session.widget
-  })),
-      container = _render.container,
-      getByText = _render.getByText;
-
-  expect(container.firstChild).toMatchSnapshot();
-  expect(getByText('ctgA:3..102 (+)')).toBeTruthy();
-});

package/dist/BamAdapter/BamAdapter.test.js

@@ -1,177 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-var _BamAdapter = _interopRequireDefault(require("./BamAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch features from volvox.bam', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, features, featuresArray, featuresJsonArray, adapterCSI, featuresCSI, featuresArrayCSI, featuresJsonArrayCSI;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _BamAdapter.default(_configSchema.default.create({
-            bamLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-              locationType: 'LocalPathLocation'
-            },
-            index: {
-              location: {
-                localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-                locationType: 'LocalPathLocation'
-              }
-            }
-          }));
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context.sent;
-          expect(featuresArray[0].get('refName')).toBe('ctgA');
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.length).toEqual(3809);
-          expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot();
-          expect(adapter.refIdToName(0)).toBe('ctgA');
-          expect(adapter.refIdToName(1)).toBe(undefined);
-          _context.t0 = expect;
-          _context.next = 14;
-          return adapter.hasDataForRefName('ctgA');
-
-        case 14:
-          _context.t1 = _context.sent;
-          (0, _context.t0)(_context.t1).toBe(true);
-          adapterCSI = new _BamAdapter.default(_configSchema.default.create({
-            bamLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-              locationType: 'LocalPathLocation'
-            },
-            index: {
-              indexType: 'CSI',
-              location: {
-                localPath: require.resolve('../../test_data/volvox-sorted.bam.csi'),
-                locationType: 'LocalPathLocation'
-              }
-            }
-          }));
-          featuresCSI = adapterCSI.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 20;
-          return featuresCSI.pipe((0, _operators.toArray)()).toPromise();
-
-        case 20:
-          featuresArrayCSI = _context.sent;
-          featuresJsonArrayCSI = featuresArrayCSI.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArrayCSI).toEqual(featuresJsonArray);
-
-        case 23:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));
-test('test usage of BamSlightlyLazyFeature toJSON (used in the widget)', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var adapter, features, featuresArray, f;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          adapter = new _BamAdapter.default(_configSchema.default.create({
-            bamLocation: {
-              localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-              locationType: 'LocalPathLocation'
-            },
-            index: {
-              location: {
-                localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-                locationType: 'LocalPathLocation'
-              },
-              indexType: 'BAI'
-            }
-          }));
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 100
-          });
-          _context2.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context2.sent;
-          f = featuresArray[0].toJSON();
-          expect(f.refName).toBe('ctgA');
-          expect(f.start).toBe(2);
-          expect(f.end).toBe(102);
-          expect(f.mismatches).not.toBeTruthy();
-
-        case 10:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));
-test('test usage of BamSlightlyLazyFeature for extended CIGAR', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-  var adapter, features, featuresArray, f;
-  return _regenerator.default.wrap(function _callee3$(_context3) {
-    while (1) {
-      switch (_context3.prev = _context3.next) {
-        case 0:
-          adapter = new _BamAdapter.default(_configSchema.default.create({
-            bamLocation: {
-              localPath: require.resolve('../../test_data/extended_cigar.bam'),
-              locationType: 'LocalPathLocation'
-            },
-            index: {
-              location: {
-                localPath: require.resolve('../../test_data/extended_cigar.bam.bai'),
-                locationType: 'LocalPathLocation'
-              },
-              indexType: 'BAI'
-            }
-          }));
-          features = adapter.getFeatures({
-            assemblyName: 'hg19',
-            refName: '1',
-            start: 13260,
-            end: 13340
-          });
-          _context3.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context3.sent;
-          f = featuresArray[0];
-          expect(f.get('mismatches')).toMatchSnapshot();
-
-        case 7:
-        case "end":
-          return _context3.stop();
-      }
-    }
-  }, _callee3);
-})));

package/dist/BamAdapter/MismatchParser.test.js

@@ -1,251 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _MismatchParser = require("./MismatchParser");
-
-var seq = 'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTT'; // examples come from https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-// and http://seqanswers.com/forums/showthread.php?t=8978
-
-test('cigar to mismatches', function () {
-  expect((0, _MismatchParser.cigarToMismatches)((0, _MismatchParser.parseCigar)('56M1D45M'), seq)).toEqual([{
-    start: 56,
-    type: 'deletion',
-    base: '*',
-    length: 1
-  }]);
-});
-test('md to mismatches', function () {
-  var cigarMismatches = (0, _MismatchParser.cigarToMismatches)((0, _MismatchParser.parseCigar)('56M1D45M'), seq);
-  expect((0, _MismatchParser.mdToMismatches)('10A80', (0, _MismatchParser.parseCigar)('56M1D45M'), cigarMismatches, seq)).toEqual([{
-    start: 10,
-    type: 'mismatch',
-    base: 'C',
-    altbase: 'A',
-    length: 1
-  }]);
-});
-describe('get mismatches', function () {
-  it('simple deletion', function () {
-    // simple deletion
-    expect((0, _MismatchParser.getMismatches)('56M1D45M', '56^A45', seq)).toEqual([{
-      start: 56,
-      type: 'deletion',
-      base: '*',
-      length: 1
-    }]);
-  });
-  it('simple insertion', function () {
-    // simple insertion
-    expect((0, _MismatchParser.getMismatches)('89M1I11M', '100', 'AAAAAAAAAACAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTA')).toEqual([{
-      start: 89,
-      type: 'insertion',
-      base: '1',
-      length: 0
-    }]);
-  });
-  it('deletion and a SNP', function () {
-    // contains a deletion and a SNP
-    // read GGGGG--ATTTTTT
-    //      |||||   ||||||
-    //      GGGGGACCTTTTTT
-    expect((0, _MismatchParser.getMismatches)('5M2D6M', '5^AC0C5', 'GGGGGATTTTTT')).toEqual([{
-      start: 5,
-      type: 'deletion',
-      base: '*',
-      length: 2
-    }, {
-      start: 7,
-      type: 'mismatch',
-      base: 'A',
-      altbase: 'C',
-      length: 1
-    }]);
-  });
-  it('0-length MD entries', function () {
-    // 0-length MD entries, which indicates two SNPs right next to each other
-    // "They generally occur between SNPs, or between a deletion then a SNP."
-    // http://seqanswers.com/forums/showthread.php?t=8978
-    //
-    // read GGGGGCATTTTT
-    //      |||||  |||||
-    // ref  GGGGGACTTTTT
-    expect((0, _MismatchParser.getMismatches)('12M', '5A0C5', 'GGGGGCATTTTT')).toEqual([{
-      altbase: 'A',
-      base: 'C',
-      length: 1,
-      start: 5,
-      type: 'mismatch'
-    }, {
-      altbase: 'C',
-      base: 'A',
-      length: 1,
-      start: 6,
-      type: 'mismatch'
-    }]);
-  });
-  it('non-0-length-MD string', function () {
-    // same as above but with the non-0-length MD string
-    // not sure if it is entirely legal, but may appear in the wild
-    expect((0, _MismatchParser.getMismatches)('12M', '5AC5', 'GGGGGCATTTTT')).toEqual([{
-      altbase: 'A',
-      base: 'C',
-      length: 1,
-      start: 5,
-      type: 'mismatch'
-    }, {
-      altbase: 'C',
-      base: 'A',
-      length: 1,
-      start: 6,
-      type: 'mismatch'
-    }]);
-  });
-});
-test('basic skip', function () {
-  expect((0, _MismatchParser.getMismatches)('6M200N6M', '5AC5', 'GGGGGCATTTTT')).toEqual([{
-    base: 'N',
-    length: 200,
-    start: 6,
-    type: 'skip'
-  }, {
-    altbase: 'A',
-    base: 'C',
-    length: 1,
-    start: 5,
-    type: 'mismatch'
-  }, {
-    altbase: 'C',
-    base: 'A',
-    length: 1,
-    start: 206,
-    type: 'mismatch'
-  }]);
-});
-test('vsbuffalo', function () {
-  // https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-  // example 1
-  expect((0, _MismatchParser.getMismatches)('89M1I11M', '100', 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA')).toEqual([{
-    base: '1',
-    length: 0,
-    start: 89,
-    type: 'insertion'
-  }]); // https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files
-  // example 2
-
-  expect((0, _MismatchParser.getMismatches)('9M1I91M', '48T42G8', 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA')).toEqual([{
-    base: '1',
-    length: 0,
-    start: 9,
-    type: 'insertion'
-  }, {
-    altbase: 'T',
-    base: 'A',
-    length: 1,
-    start: 48,
-    type: 'mismatch'
-  }, {
-    altbase: 'G',
-    base: 'A',
-    length: 1,
-    start: 91,
-    type: 'mismatch'
-  }]);
-});
-test('more skip', function () {
-  expect((0, _MismatchParser.getMismatches)('3M200N3M200N3M', '8A', 'GGGGGCATTTTT')).toEqual([{
-    base: 'N',
-    length: 200,
-    start: 3,
-    type: 'skip'
-  }, {
-    base: 'N',
-    length: 200,
-    start: 206,
-    type: 'skip'
-  }, {
-    altbase: 'A',
-    base: 'T',
-    length: 1,
-    start: 408,
-    type: 'mismatch'
-  }]);
-  expect((0, _MismatchParser.getMismatches)('31M1I17M1D37M', '6G4C20G1A5C5A1^C3A15G1G15', seq).sort(function (a, b) {
-    return a.start - b.start;
-  })).toMatchInlineSnapshot("\n    Array [\n      Object {\n        \"altbase\": \"G\",\n        \"base\": \"A\",\n        \"length\": 1,\n        \"start\": 6,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"C\",\n        \"base\": \"A\",\n        \"length\": 1,\n        \"start\": 11,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"base\": \"1\",\n        \"length\": 0,\n        \"start\": 31,\n        \"type\": \"insertion\",\n      },\n      Object {\n        \"altbase\": \"G\",\n        \"base\": \"C\",\n        \"length\": 1,\n        \"start\": 32,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"A\",\n        \"base\": \"C\",\n        \"length\": 1,\n        \"start\": 34,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"C\",\n        \"base\": \"C\",\n        \"length\": 1,\n        \"start\": 40,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"A\",\n        \"base\": \"C\",\n        \"length\": 1,\n        \"start\": 46,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"base\": \"*\",\n        \"length\": 1,\n        \"start\": 48,\n        \"type\": \"deletion\",\n      },\n      Object {\n        \"altbase\": \"A\",\n        \"base\": \"G\",\n        \"length\": 1,\n        \"start\": 52,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"G\",\n        \"base\": \"G\",\n        \"length\": 1,\n        \"start\": 68,\n        \"type\": \"mismatch\",\n      },\n      Object {\n        \"altbase\": \"G\",\n        \"base\": \"G\",\n        \"length\": 1,\n        \"start\": 70,\n        \"type\": \"mismatch\",\n      },\n    ]\n  ");
-});
-test('clipping', function () {
-  expect((0, _MismatchParser.getMismatches)('200H10M200H', '9A', 'AAAAAAAAAC')).toEqual([{
-    cliplen: 200,
-    base: 'H200',
-    length: 1,
-    start: 0,
-    type: 'hardclip'
-  }, {
-    cliplen: 200,
-    base: 'H200',
-    length: 1,
-    start: 10,
-    type: 'hardclip'
-  }, {
-    altbase: 'A',
-    base: 'C',
-    length: 1,
-    start: 9,
-    type: 'mismatch'
-  }]);
-  expect((0, _MismatchParser.getMismatches)('10S10M10S', '9A', 'AAAAAAAAAAGGGGGGGGGC')).toEqual([{
-    cliplen: 10,
-    base: 'S10',
-    length: 1,
-    start: 0,
-    type: 'softclip'
-  }, {
-    cliplen: 10,
-    base: 'S10',
-    length: 1,
-    start: 10,
-    type: 'softclip'
-  }, {
-    altbase: 'A',
-    base: 'C',
-    length: 1,
-    start: 9,
-    type: 'mismatch'
-  }]);
-});
-test('getNextRefPos test 1', function () {
-  var cigar = (0, _MismatchParser.parseCigar)('10S10M1I4M1D15M');
-  var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15, 20, 25, 30, 35]);
-  expect((0, _toConsumableArray2.default)(iter)).toEqual([0, 5, 15, 20, 25]);
-});
-test('getNextRefPos test 2', function () {
-  var cigar = (0, _MismatchParser.parseCigar)('10S15M');
-  var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15]);
-  expect((0, _toConsumableArray2.default)(iter)).toEqual([0, 5]);
-});
-test('getModificationPositions', function () {
-  var positions = (0, _MismatchParser.getModificationPositions)('C+m,2,2,1,4,1', 'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA', 1);
-  expect(positions[0]).toEqual({
-    type: 'm',
-    positions: [6, 17, 20, 31, 34]
-  });
-}); // ? means "modification status of the skipped bases provided."
-
-test('getModificationPositions with unknown (?)', function () {
-  var positions = (0, _MismatchParser.getModificationPositions)('C+m?,2,2,1,4,1', 'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA', 1);
-  expect(positions[0]).toEqual({
-    type: 'm',
-    positions: [6, 17, 20, 31, 34]
-  });
-}); // . means "modification status of the skipped bases is low probability"
-
-test('getModificationPositions with unknown (.)', function () {
-  var positions = (0, _MismatchParser.getModificationPositions)('C+m.,2,2,1,4,1', 'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA', 1);
-  expect(positions[0]).toEqual({
-    type: 'm',
-    positions: [6, 17, 20, 31, 34]
-  });
-});