@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/src/util.ts

@@ -1,154 +0,0 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Feature, AugmentedRegion } from '@jbrowse/core/util'
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import { IAnyStateTreeNode, addDisposer, isAlive } from 'mobx-state-tree'
-import { IAutorunOptions, autorun } from 'mobx'
-
-// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
-// BAM does not
-export function getTag(feature: Feature, tag: string) {
-  const tags = feature.get('tags')
-  return tags !== undefined ? tags[tag] : feature.get(tag)
-}
-
-// use fallback alt tag, used in situations where upper case/lower case tags
-// exist e.g. Mm/MM for base modifications
-export function getTagAlt(feature: Feature, tag: string, alt: string) {
-  return getTag(feature, tag) ?? getTag(feature, alt)
-}
-
-// orientation definitions from igv.js, see also
-// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
-export const orientationTypes = {
-  fr: {
-    F1R2: 'LR',
-    F2R1: 'LR',
-
-    F1F2: 'LL',
-    F2F1: 'LL',
-
-    R1R2: 'RR',
-    R2R1: 'RR',
-
-    R1F2: 'RL',
-    R2F1: 'RL',
-  } as { [key: string]: string },
-
-  rf: {
-    R1F2: 'LR',
-    R2F1: 'LR',
-
-    R1R2: 'LL',
-    R2R1: 'LL',
-
-    F1F2: 'RR',
-    F2F1: 'RR',
-
-    F1R2: 'RL',
-    F2R1: 'RL',
-  } as { [key: string]: string },
-
-  ff: {
-    F2F1: 'LR',
-    R1R2: 'LR',
-
-    F2R1: 'LL',
-    R1F2: 'LL',
-
-    R2F1: 'RR',
-    F1R2: 'RR',
-
-    R2R1: 'RL',
-    F1F2: 'RL',
-  } as { [key: string]: string },
-}
-
-export const pairMap = {
-  LR: 'color_pair_lr',
-  LL: 'color_pair_ll',
-  RR: 'color_pair_rr',
-  RL: 'color_pair_rl',
-} as const
-
-export function getColorWGBS(strand: number, base: string) {
-  if (strand === 1) {
-    if (base === 'C') {
-      return '#f00'
-    }
-    if (base === 'T') {
-      return '#00f'
-    }
-  } else if (strand === -1) {
-    if (base === 'G') {
-      return '#f00'
-    }
-    if (base === 'A') {
-      return '#00f'
-    }
-  }
-  return '#888'
-}
-
-// fetches region sequence augmenting by +/- 1bp for CpG on either side of
-// requested region
-export async function fetchSequence(
-  region: AugmentedRegion,
-  adapter: BaseFeatureDataAdapter,
-) {
-  const { start, end, originalRefName, refName } = region
-
-  const feats = await firstValueFrom(
-    adapter
-      .getFeatures({
-        ...region,
-        refName: originalRefName || refName,
-        end: end + 1,
-        start: Math.max(0, start - 1),
-      })
-      .pipe(toArray()),
-  )
-  return feats[0]?.get('seq')
-}
-
-// has to check underlying C-G (aka CpG) on the reference sequence
-export function shouldFetchReferenceSequence(type?: string) {
-  return type === 'methylation'
-}
-
-// adapted from IGV
-// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
-export const modificationColors = {
-  m: 'rgb(255,0,0)',
-  h: 'rgb(11, 132, 165)',
-  o: 'rgb(111, 78, 129)',
-  f: 'rgb(246, 200, 95)',
-  c: 'rgb(157, 216, 102)',
-  g: 'rgb(255, 160, 86)',
-  e: 'rgb(141, 221, 208)',
-  b: 'rgb(202, 71, 47)',
-} as Record<string, string | undefined>
-
-type DisplayModel = IAnyStateTreeNode & { setError: (arg: unknown) => void }
-
-export function createAutorun(
-  self: DisplayModel,
-  cb: () => Promise<void>,
-  opts?: IAutorunOptions,
-) {
-  addDisposer(
-    self,
-    autorun(async () => {
-      try {
-        await cb()
-      } catch (e) {
-        if (isAlive(self)) {
-          self.setError(e)
-        }
-      }
-    }, opts),
-  )
-}
-export function randomColor() {
-  return `hsl(${Math.random() * 200}, 50%, 50%)`
-}