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const tags = {\n  AM: 'The smallest template-independent mapping quality in the template',\n  AS: 'Alignment score generated by aligner',\n  BC: 'Barcode sequence identifying the sample',\n  BQ: 'Offset to base alignment quality (BAQ)',\n  BZ: 'Phred quality of the unique molecular barcode bases in the {OX} tag',\n  CB: 'Cell identifier',\n  CC: 'Reference name of the next hit',\n  CM: 'Edit distance between the color sequence and the color reference (see also {NM})',\n  CO: 'Free-text comments',\n  CP: 'Leftmost coordinate of the next hit',\n  CQ: 'Color read base qualities',\n  CR: 'Cellular barcode sequence bases (uncorrected)',\n  CS: 'Color read sequence',\n  CT: 'Complete read annotation tag, used for consensus annotation dummy features',\n  CY: 'Phred quality of the cellular barcode sequence in the {CR} tag',\n  E2: 'The 2nd most likely base calls',\n  FI: 'The index of segment in the template',\n  FS: 'Segment suffix',\n  FZ: 'Flow signal intensities',\n  GC: 'Reserved for backwards compatibility reasons',\n  GQ: 'Reserved for backwards compatibility reasons',\n  GS: 'Reserved for backwards compatibility reasons',\n  H0: 'Number of perfect hits',\n  H1: 'Number of 1-difference hits (see also {NM})',\n  H2: 'Number of 2-difference hits',\n  HI: 'Query hit index',\n  IH: 'Query hit total count',\n  LB: 'Library',\n  MC: 'CIGAR string for mate/next segment',\n  MD: 'String encoding mismatched and deleted reference bases',\n  MF: 'Reserved for backwards compatibility reasons',\n  MI: 'Molecular identifier; a string that uniquely identifies the molecule from which the record was derived',\n  ML: 'Base modification probabilities',\n  MM: 'Base modifications / methylation ',\n  MQ: 'Mapping quality of the mate/next segment',\n  NH: 'Number of reported alignments that contain the query in the current record',\n  NM: 'Edit distance to the reference',\n  OA: 'Original alignment',\n  OC: 'Original CIGAR (deprecated; use {OA} instead)',\n  OP: 'Original mapping position (deprecated; use {OA} instead)',\n  OQ: 'Original base quality',\n  OX: 'Original unique molecular barcode bases',\n  PG: 'Program',\n  PQ: 'Phred likelihood of the template',\n  PT: 'Read annotations for parts of the padded read sequence',\n  PU: 'Platform unit',\n  Q2: 'Phred quality of the mate/next segment sequence in the {R2} tag',\n  QT: 'Phred quality of the sample barcode sequence in the {BC} tag',\n  QX: 'Quality score of the unique molecular identifier in the {RX} tag',\n  R2: 'Sequence of the mate/next segment in the template',\n  RG: 'Read group',\n  RT: 'Reserved for backwards compatibility reasons',\n  RX: 'Sequence bases of the (possibly corrected) unique molecular identifier',\n  S2: 'Reserved for backwards compatibility reasons',\n  SA: 'Other canonical alignments in a chimeric alignment',\n  SM: 'Template-independent mapping quality',\n  SQ: 'Reserved for backwards compatibility reasons',\n  TC: 'The number of segments in the template',\n  TS: 'Transcript strand',\n  U2: 'Phred probability of the 2nd call being wrong conditional on the best being wrong',\n  UQ: 'Phred likelihood of the segment, conditional on the mapping being correct',\n}\n","import React from 'react'\nimport { Checkbox, FormControlLabel, FormGroup } from '@mui/material'\nimport { makeStyles } from 'tss-react/mui'\nimport { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'\nimport SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField'\n\nconst useStyles = makeStyles()({\n  compact: {\n    paddingRight: 0,\n    paddingTop: 0,\n    paddingBottom: 0,\n  },\n})\n\nconst flagNames = [\n  'read paired',\n  'read mapped in proper pair',\n  'read unmapped',\n  'mate unmapped',\n  'read reverse strand',\n  'mate reverse strand',\n  'first in pair',\n  'second in pair',\n  'not primary alignment',\n  'read fails platform/vendor quality checks',\n  'read is PCR or optical duplicate',\n  'supplementary alignment',\n]\n\nexport default function AlignmentFlags(props: { feature: { flags: number } }) {\n  const { classes } = useStyles()\n  const { feature } = props\n  const { flags } = feature\n\n  return (\n    <BaseCard {...props} title=\"Flags\">\n      <SimpleField name=\"Flag\" value={flags} />\n      <FormGroup>\n        {flagNames.map((name, idx) => {\n          const val = flags & (1 << idx)\n          const key = `${name}_${val}`\n          return (\n            <FormControlLabel\n              key={key}\n              control={\n                <Checkbox\n                  className={classes.compact}\n                  checked={Boolean(val)}\n                  name={name}\n                  readOnly\n                />\n              }\n              label={name}\n            />\n          )\n        })}\n      </FormGroup>\n    </BaseCard>\n  )\n}\n","import React from 'react'\nimport { Link } from '@mui/material'\n\n// locals\nimport { AlignmentFeatureWidgetModel } from './stateModelFactory'\nimport { navToLoc } from './util'\n\nexport default function PairLink({\n  locString,\n  model,\n}: {\n  locString: string\n  model: AlignmentFeatureWidgetModel\n}) {\n  return (\n    <Link\n      onClick={event => {\n        event.preventDefault()\n        // eslint-disable-next-line @typescript-eslint/no-floating-promises\n        navToLoc(locString, model)\n      }}\n      href=\"#\"\n    >\n      {locString}\n    </Link>\n  )\n}\n","import React, { useState } from 'react'\nimport copy from 'copy-to-clipboard'\n\n// this 'show more...' used specifically as a formatter on alignments feature\n// details because long SEQ or CRAM files, even a single div full of a ton of\n// data from a long read, can slow down the rest of the app\nexport default function Formatter({ value }: { value: unknown }) {\n  const [show, setShow] = useState(false)\n  const [copied, setCopied] = useState(false)\n  const display = String(value)\n  return display.length > 100 ? (\n    <>\n      <button\n        type=\"button\"\n        onClick={() => {\n          copy(display)\n          setCopied(true)\n          setTimeout(() => {\n            setCopied(false)\n          }, 700)\n        }}\n      >\n        {copied ? 'Copied to clipboard' : 'Copy'}\n      </button>\n      <button\n        type=\"button\"\n        onClick={() => {\n          setShow(val => !val)\n        }}\n      >\n        {show ? 'Show less' : 'Show more'}\n      </button>\n      <div>{show ? display : `${display.slice(0, 100)}...`}</div>\n    </>\n  ) : (\n    <div>{display}</div>\n  )\n}\n","import React, { lazy } from 'react'\nimport { Paper } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport clone from 'clone'\nimport { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'\n\n// locals\nimport { getTag } from './util'\nimport { tags } from './tagInfo'\nimport { AlignmentFeatureWidgetModel } from './stateModelFactory'\n\n// local components\nimport Flags from './Flags'\nimport PairLink from './PairLink'\nimport Formatter from './Formatter'\n\n// lazies\nconst SupplementaryAlignments = lazy(() => import('./SupplementaryAlignments'))\nconst LinkedPairedAlignments = lazy(() => import('./LinkedPairedAlignments'))\n\nconst omit = ['clipPos', 'flags']\n\nconst AlignmentsFeatureDetails = observer(function (props: {\n  model: AlignmentFeatureWidgetModel\n}) {\n  const { model } = props\n  const { featureData } = model\n  const feat = clone(featureData)\n  const SA = getTag('SA', feat) as string | undefined\n  const { flags } = feat\n  return (\n    <Paper data-testid=\"alignment-side-drawer\">\n      <FeatureDetails\n        {...props}\n        omit={omit}\n        // @ts-expect-error\n        descriptions={{ ...tags, tags: tags }}\n        feature={feat}\n        formatter={(value, key) =>\n          key === 'next_segment_position' ? (\n            <PairLink model={model} locString={value as string} />\n          ) : (\n            <Formatter value={value} />\n          )\n        }\n      />\n      {SA !== undefined ? (\n        <SupplementaryAlignments model={model} tag={SA} feature={feat} />\n      ) : null}\n      {flags & 1 ? (\n        <LinkedPairedAlignments model={model} feature={feat} />\n      ) : null}\n\n      {flags !== undefined ? <Flags feature={feat} {...props} /> : null}\n    </Paper>\n  )\n})\n\nexport default AlignmentsFeatureDetails\n","import { getSession } from '@jbrowse/core/util'\nimport { IAnyStateTreeNode } from 'mobx-state-tree'\n\nexport function getTag(\n  tag: string,\n  feat: {\n    tags?: Record<string, unknown>\n    [key: string]: unknown\n  },\n) {\n  return feat.tags?.[tag] || feat[tag]\n}\n\nexport async function navToLoc(locString: string, model: IAnyStateTreeNode) {\n  const session = getSession(model)\n  const { view } = model\n  try {\n    if (view) {\n      await view.navToLocString(locString)\n    } else {\n      throw new Error('No view associated with this view anymore')\n    }\n  } catch (e) {\n    console.error(e)\n    session.notify(`${e}`)\n  }\n}\n"],"names":["tags","AM","AS","BC","BQ","BZ","CB","CC","CM","CO","CP","CQ","CR","CS","CT","CY","E2","FI","FS","FZ","GC","GQ","GS","H0","H1","H2","HI","IH","LB","MC","MD","MF","MI","ML","MM","MQ","NH","NM","OA","OC","OP","OQ","OX","PG","PQ","PT","PU","Q2","QT","QX","R2","RG","RT","RX","S2","SA","SM","SQ","TC","TS","U2","UQ","useStyles","makeStyles","compact","paddingRight","paddingTop","paddingBottom","flagNames","AlignmentFlags","props","classes","feature","flags","React","BaseCard","_extends","title","SimpleField","name","value","FormGroup","map","idx","val","key","FormControlLabel","control","Checkbox","className","checked","Boolean","readOnly","label","PairLink","locString","model","Link","onClick","event","preventDefault","navToLoc","href","Formatter","show","setShow","useState","copied","setCopied","display","String","length","type","copy","setTimeout","slice","SupplementaryAlignments","lazy","LinkedPairedAlignments","omit","observer","featureData","feat","clone","getTag","Paper","FeatureDetails","descriptions","formatter","undefined","tag","Flags","async","session","getSession","view","Error","navToLocString","e","console","error","notify"],"sourceRoot":""}
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