@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/esm/shared/fetchChains.js.map

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package/esm/shared/index.js.map

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package/esm/shared/renderSvg.js.map

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package/esm/shared/util.js.map

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package/esm/util.js.map

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package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx

@@ -1,155 +0,0 @@
-import React, { useState } from 'react'
-import { Link, Paper } from '@mui/material'
-import { observer } from 'mobx-react'
-import copy from 'copy-to-clipboard'
-import clone from 'clone'
-import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
-import { IAnyStateTreeNode } from 'mobx-state-tree'
-
-// locals
-import { getTag, navToLoc } from './util'
-import SupplementaryAlignments from './AlignmentsFeatureSuppAligns'
-import AlignmentFlags from './AlignmentsFeatureFlags'
-
-const omit = ['clipPos', 'flags']
-
-const tags = {
-  AM: 'The smallest template-independent mapping quality in the template',
-  AS: 'Alignment score generated by aligner',
-  BC: 'Barcode sequence identifying the sample',
-  BQ: 'Offset to base alignment quality (BAQ)',
-  BZ: 'Phred quality of the unique molecular barcode bases in the {OX} tag',
-  CB: 'Cell identifier',
-  CC: 'Reference name of the next hit',
-  CM: 'Edit distance between the color sequence and the color reference (see also {NM})',
-  CO: 'Free-text comments',
-  CP: 'Leftmost coordinate of the next hit',
-  CQ: 'Color read base qualities',
-  CR: 'Cellular barcode sequence bases (uncorrected)',
-  CS: 'Color read sequence',
-  CT: 'Complete read annotation tag, used for consensus annotation dummy features',
-  CY: 'Phred quality of the cellular barcode sequence in the {CR} tag',
-  E2: 'The 2nd most likely base calls',
-  FI: 'The index of segment in the template',
-  FS: 'Segment suffix',
-  FZ: 'Flow signal intensities',
-  GC: 'Reserved for backwards compatibility reasons',
-  GQ: 'Reserved for backwards compatibility reasons',
-  GS: 'Reserved for backwards compatibility reasons',
-  H0: 'Number of perfect hits',
-  H1: 'Number of 1-difference hits (see also {NM})',
-  H2: 'Number of 2-difference hits',
-  HI: 'Query hit index',
-  IH: 'Query hit total count',
-  LB: 'Library',
-  MC: 'CIGAR string for mate/next segment',
-  MD: 'String encoding mismatched and deleted reference bases',
-  MF: 'Reserved for backwards compatibility reasons',
-  MI: 'Molecular identifier; a string that uniquely identifies the molecule from which the record was derived',
-  ML: 'Base modification probabilities',
-  MM: 'Base modifications / methylation ',
-  MQ: 'Mapping quality of the mate/next segment',
-  NH: 'Number of reported alignments that contain the query in the current record',
-  NM: 'Edit distance to the reference',
-  OA: 'Original alignment',
-  OC: 'Original CIGAR (deprecated; use {OA} instead)',
-  OP: 'Original mapping position (deprecated; use {OA} instead)',
-  OQ: 'Original base quality',
-  OX: 'Original unique molecular barcode bases',
-  PG: 'Program',
-  PQ: 'Phred likelihood of the template',
-  PT: 'Read annotations for parts of the padded read sequence',
-  PU: 'Platform unit',
-  Q2: 'Phred quality of the mate/next segment sequence in the {R2} tag',
-  QT: 'Phred quality of the sample barcode sequence in the {BC} tag',
-  QX: 'Quality score of the unique molecular identifier in the {RX} tag',
-  R2: 'Sequence of the mate/next segment in the template',
-  RG: 'Read group',
-  RT: 'Reserved for backwards compatibility reasons',
-  RX: 'Sequence bases of the (possibly corrected) unique molecular identifier',
-  S2: 'Reserved for backwards compatibility reasons',
-  SA: 'Other canonical alignments in a chimeric alignment',
-  SM: 'Template-independent mapping quality',
-  SQ: 'Reserved for backwards compatibility reasons',
-  TC: 'The number of segments in the template',
-  TS: 'Transcript strand',
-  U2: 'Phred probability of the 2nd call being wrong conditional on the best being wrong',
-  UQ: 'Phred likelihood of the segment, conditional on the mapping being correct',
-}
-
-function Formatter({ value }: { value: unknown }) {
-  const [show, setShow] = useState(false)
-  const [copied, setCopied] = useState(false)
-  const display = String(value)
-  return display.length > 100 ? (
-    <>
-      <button
-        type="button"
-        onClick={() => {
-          copy(display)
-          setCopied(true)
-          setTimeout(() => setCopied(false), 700)
-        }}
-      >
-        {copied ? 'Copied to clipboard' : 'Copy'}
-      </button>
-      <button type="button" onClick={() => setShow(val => !val)}>
-        {show ? 'Show less' : 'Show more'}
-      </button>
-      <div>{show ? display : `${display.slice(0, 100)}...`}</div>
-    </>
-  ) : (
-    <div>{display}</div>
-  )
-}
-
-function PairLink({
-  locString,
-  model,
-}: {
-  locString: string
-  model: IAnyStateTreeNode
-}) {
-  return (
-    <Link
-      onClick={event => {
-        event.preventDefault()
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        navToLoc(locString, model)
-      }}
-      href="#"
-    >
-      {locString}
-    </Link>
-  )
-}
-
-export default observer(function AlignmentFeatureDetails(props: {
-  model: IAnyStateTreeNode
-}) {
-  const { model } = props
-  const feat = clone(model.featureData)
-  const SA = getTag('SA', feat) as string
-  return (
-    <Paper data-testid="alignment-side-drawer">
-      <FeatureDetails
-        {...props}
-        omit={omit}
-        // @ts-expect-error
-        descriptions={{ ...tags, tags }}
-        feature={feat}
-        formatter={(value, key) =>
-          key === 'next_segment_position' ? (
-            <PairLink model={model} locString={value as string} />
-          ) : (
-            <Formatter value={value} />
-          )
-        }
-      />
-      {SA ? <SupplementaryAlignments model={model} tag={SA} /> : null}
-      {feat.flags !== undefined ? (
-        <AlignmentFlags feature={feat} {...props} />
-      ) : null}
-    </Paper>
-  )
-})

package/src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx

@@ -1,60 +0,0 @@
-import React from 'react'
-import { Checkbox, FormControlLabel, FormGroup } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
-import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField'
-
-const useStyles = makeStyles()({
-  compact: {
-    paddingRight: 0,
-    paddingTop: 0,
-    paddingBottom: 0,
-  },
-})
-
-const flagNames = [
-  'read paired',
-  'read mapped in proper pair',
-  'read unmapped',
-  'mate unmapped',
-  'read reverse strand',
-  'mate reverse strand',
-  'first in pair',
-  'second in pair',
-  'not primary alignment',
-  'read fails platform/vendor quality checks',
-  'read is PCR or optical duplicate',
-  'supplementary alignment',
-]
-
-export default function AlignmentFlags(props: { feature: { flags: number } }) {
-  const { classes } = useStyles()
-  const { feature } = props
-  const { flags } = feature
-
-  return (
-    <BaseCard {...props} title="Flags">
-      <SimpleField name="Flag" value={flags} />
-      <FormGroup>
-        {flagNames.map((name, idx) => {
-          const val = flags & (1 << idx)
-          const key = `${name}_${val}`
-          return (
-            <FormControlLabel
-              key={key}
-              control={
-                <Checkbox
-                  className={classes.compact}
-                  checked={Boolean(val)}
-                  name={name}
-                  readOnly
-                />
-              }
-              label={name}
-            />
-          )
-        })}
-      </FormGroup>
-    </BaseCard>
-  )
-}

package/src/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.tsx

@@ -1,51 +0,0 @@
-import React from 'react'
-import { Typography, Link } from '@mui/material'
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
-import { getLengthOnRef } from '../MismatchParser'
-import { IAnyStateTreeNode } from 'mobx-state-tree'
-import { navToLoc } from './util'
-
-export default function SupplementaryAlignments(props: {
-  tag: string
-  model: IAnyStateTreeNode
-}) {
-  const { tag, model } = props
-  return (
-    <BaseCard {...props} title="Supplementary alignments">
-      <Typography>List of supplementary alignment locations</Typography>
-      <ul>
-        {tag
-          .split(';')
-          .filter(SA => !!SA)
-          .map((SA, index) => {
-            const [saRef, saStart, saStrand, saCigar] = SA.split(',')
-            const saLength = getLengthOnRef(saCigar)
-            const extra = Math.floor(saLength / 5)
-            const start = +saStart
-            const end = +saStart + saLength
-            const locString = `${saRef}:${Math.max(1, start - extra)}-${
-              end + extra
-            }`
-            const displayStart = start.toLocaleString('en-US')
-            const displayEnd = end.toLocaleString('en-US')
-            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`
-            return (
-              <li key={`${locString}-${index}`}>
-                <Link
-                  onClick={async event => {
-                    event.preventDefault()
-
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    navToLoc(locString, model)
-                  }}
-                  href="#"
-                >
-                  {displayString}
-                </Link>
-              </li>
-            )
-          })}
-      </ul>
-    </BaseCard>
-  )
-}

package/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap

@@ -1,327 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`open up a widget 1`] = `
-<div
-  class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 css-1ps6pg7-MuiPaper-root"
-  data-testid="alignment-side-drawer"
->
-  <div
-    class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 MuiAccordion-root MuiAccordion-rounded Mui-expanded MuiAccordion-gutters css-1elwnq4-MuiPaper-root-MuiAccordion-root"
-  >
-    <div
-      aria-expanded="true"
-      class="MuiButtonBase-root MuiAccordionSummary-root Mui-expanded MuiAccordionSummary-gutters css-sh22l5-MuiButtonBase-root-MuiAccordionSummary-root"
-      role="button"
-      tabindex="0"
-    >
-      <div
-        class="MuiAccordionSummary-content Mui-expanded MuiAccordionSummary-contentGutters css-o4b71y-MuiAccordionSummary-content"
-      >
-        <span
-          class="MuiTypography-root MuiTypography-button css-1f0on15-MuiTypography-root"
-        >
-           
-          ctgA_3_555_0:0:0_2:0... - match
-        </span>
-      </div>
-      <div
-        class="MuiAccordionSummary-expandIconWrapper Mui-expanded css-yw020d-MuiAccordionSummary-expandIconWrapper"
-      >
-        <svg
-          aria-hidden="true"
-          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-ymsoo8-MuiSvgIcon-root-expandIcon"
-          data-testid="ExpandMoreIcon"
-          focusable="false"
-          viewBox="0 0 24 24"
-        >
-          <path
-            d="M16.59 8.59 12 13.17 7.41 8.59 6 10l6 6 6-6z"
-          />
-        </svg>
-      </div>
-    </div>
-    <div
-      class="MuiCollapse-root MuiCollapse-vertical MuiCollapse-entered css-pwcg7p-MuiCollapse-root"
-      style="min-height: 0px;"
-    >
-      <div
-        class="MuiCollapse-wrapper MuiCollapse-vertical css-smkl36-MuiCollapse-wrapper"
-      >
-        <div
-          class="MuiCollapse-wrapperInner MuiCollapse-vertical css-9l5vo-MuiCollapse-wrapperInner"
-        >
-          <div
-            class="MuiAccordion-region"
-            role="region"
-          >
-            <div
-              class="MuiAccordionDetails-root css-rqrb7m-MuiAccordionDetails-root-expansionPanelDetails"
-            >
-              <p
-                class="MuiTypography-root MuiTypography-body1 css-ahj2mt-MuiTypography-root"
-              >
-                Core details
-              </p>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                >
-                  Position
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  ctgA:3..102 (+)
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                >
-                  Name
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <span>
-                    ctgA_3_555_0:0:0_2:0:0_102d
-                  </span>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                >
-                  Length
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <span>
-                    100
-                  </span>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                >
-                  Type
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <span>
-                    match
-                  </span>
-                </div>
-              </div>
-              <hr
-                class="MuiDivider-root MuiDivider-fullWidth css-9mgopn-MuiDivider-root"
-              />
-              <p
-                class="MuiTypography-root MuiTypography-body1 css-ahj2mt-MuiTypography-root"
-              >
-                Attributes
-              </p>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                  style="width: 96px;"
-                >
-                  seq
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <div>
-                    TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG
-                  </div>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                  style="width: 96px;"
-                >
-                  score
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <div>
-                    37
-                  </div>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                  style="width: 96px;"
-                >
-                  qual
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <button
-                    type="button"
-                  >
-                    Copy
-                  </button>
-                  <button
-                    type="button"
-                  >
-                    Show more
-                  </button>
-                  <div>
-                    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 1...
-                  </div>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  aria-label="Mapping quality of the mate/next segment"
-                  class="css-18vnxxj-fieldDescription-fieldName"
-                  data-mui-internal-clone-element="true"
-                >
-                  MQ
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <div>
-                    37
-                  </div>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                  style="width: 96px;"
-                >
-                  CIGAR
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <div>
-                    100M
-                  </div>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                  style="width: 96px;"
-                >
-                  length_on_ref
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <div>
-                    100
-                  </div>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                  style="width: 96px;"
-                >
-                  template_length
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <div>
-                    0
-                  </div>
-                </div>
-              </div>
-              <div
-                class="css-1m8nxnb-field"
-              >
-                <div
-                  class="css-1q83rf3-fieldName"
-                  style="width: 96px;"
-                >
-                  seq_length
-                </div>
-                <div
-                  class="css-1omt041-fieldValue"
-                >
-                  <div>
-                    100
-                  </div>
-                </div>
-              </div>
-              <div
-                class="css-1lttu3w-container"
-              >
-                <button
-                  class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
-                  tabindex="0"
-                  type="button"
-                >
-                  Show feature sequence
-                  <span
-                    class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                  />
-                </button>
-                <div
-                  class="MuiFormControl-root css-147opmv-MuiFormControl-root-formControl"
-                >
-                  <button
-                    class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
-                    tabindex="0"
-                    type="button"
-                  >
-                    <svg
-                      aria-hidden="true"
-                      class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
-                      data-testid="HelpIcon"
-                      focusable="false"
-                      viewBox="0 0 24 24"
-                    >
-                      <path
-                        d="M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10S17.52 2 12 2zm1 17h-2v-2h2v2zm2.07-7.75-.9.92C13.45 12.9 13 13.5 13 15h-2v-.5c0-1.1.45-2.1 1.17-2.83l1.24-1.26c.37-.36.59-.86.59-1.41 0-1.1-.9-2-2-2s-2 .9-2 2H8c0-2.21 1.79-4 4-4s4 1.79 4 4c0 .88-.36 1.68-.93 2.25z"
-                      />
-                    </svg>
-                    <span
-                      class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-                    />
-                  </button>
-                </div>
-              </div>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-`;

package/src/AlignmentsFeatureDetail/index.test.tsx

@@ -1,47 +0,0 @@
-import React from 'react'
-import { render } from '@testing-library/react'
-import { types } from 'mobx-state-tree'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-// locals
-import { stateModelFactory } from '.'
-import ReactComponent from './AlignmentsFeatureDetail'
-
-test('open up a widget', () => {
-  const pluginManager = new PluginManager([])
-
-  const Session = types.model({
-    rpcManager: types.optional(types.frozen(), {}),
-    configuration: ConfigurationSchema('test', {}),
-    widget: stateModelFactory(pluginManager),
-  })
-  const session = Session.create(
-    {
-      // @ts-expect-error
-      widget: { type: 'AlignmentsFeatureWidget' },
-    },
-    { pluginManager },
-  )
-  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',
-  })
-  const { container, getByText } = render(
-    <ReactComponent model={session.widget} />,
-  )
-  expect(container.firstChild).toMatchSnapshot()
-  expect(getByText('ctgA:3..102 (+)')).toBeTruthy()
-})