@jbrowse/plugin-comparative-adapters 2.6.1 → 2.6.3

package/src/PAFAdapter/test_data/peach_grape.paf

@@ -1,30 +0,0 @@
-Pp01	47851208	29082916	29084251	-	chr1	23037639	33358	34714	133	1384	28	tp:A:P	cm:i:11	s1:i:118	s2:i:0	dv:f:0.2085	rl:i:921840
-Pp01	47851208	28948232	28948605	-	chr1	23037639	93405	93770	64	373	8	tp:A:P	cm:i:6	s1:i:62	s2:i:0	dv:f:0.1609	rl:i:921840
-Pp01	47851208	28945891	28946469	-	chr1	23037639	97669	98259	52	590	3	tp:A:P	cm:i:4	s1:i:50	s2:i:0	dv:f:0.2227	rl:i:921840
-Pp05	18496696	16629254	16629762	-	chr1	23037639	175180	175679	54	508	4	tp:A:P	cm:i:6	s1:i:52	s2:i:0	dv:f:0.1841	rl:i:342905
-Pp01	47851208	42403393	42405783	-	chr1	23037639	187350	189723	52	2390	1	tp:A:P	cm:i:5	s1:i:48	s2:i:45	dv:f:0.3006	rl:i:921840
-Pp01	47851208	28921887	28922054	-	chr1	23037639	206059	206226	53	167	4	tp:A:P	cm:i:5	s1:i:53	s2:i:0	dv:f:0.1149	rl:i:921840
-Pp08	22573980	13883074	13883131	-	chr1	23037639	214168	214225	57	57	1	tp:A:P	cm:i:10	s1:i:57	s2:i:54	dv:f:0.0122	rl:i:412904
-Pp01	47851208	28915197	28916072	-	chr1	23037639	221178	222026	60	881	4	tp:A:P	cm:i:4	s1:i:53	s2:i:0	dv:f:0.2468	rl:i:921840
-Pp01	47851208	28859196	28861497	+	chr1	23037639	259252	261582	209	2393	32	tp:A:P	cm:i:17	s1:i:180	s2:i:56	dv:f:0.2144	rl:i:921840
-Pp01	47851208	28870442	28871466	+	chr1	23037639	259252	260320	228	1116	36	tp:A:P	cm:i:22	s1:i:203	s2:i:50	dv:f:0.1427	rl:i:921840
-Pp01	47851208	49027	49442	-	chr8	22385789	8155257	8155673	74	416	13	tp:A:P	cm:i:7	s1:i:74	s2:i:0	dv:f:0.1632	rl:i:921840
-Pp01	47851208	50074	50181	-	chr8	22385789	8141660	8141767	45	107	1	tp:A:P	cm:i:3	s1:i:45	s2:i:0	dv:f:0.1297	rl:i:921840
-Pp01	47851208	53642	54893	+	chr8	22385789	8654487	8655674	62	1252	2	tp:A:P	cm:i:5	s1:i:51	s2:i:45	dv:f:0.2511	rl:i:921840
-Pp01	47851208	73614	73741	-	chr9	23006712	13774809	13774936	85	127	18	tp:A:P	cm:i:11	s1:i:85	s2:i:0	dv:f:0.0462	rl:i:921840
-Pp01	47851208	80728	82019	-	chr9	23006712	13695413	13696666	103	1291	23	tp:A:P	cm:i:10	s1:i:96	s2:i:0	dv:f:0.2146	rl:i:921840
-Pp01	47851208	106247	106925	+	chr18	29360087	13357403	13358082	40	679	0	tp:A:P	cm:i:5	s1:i:40	s2:i:0	dv:f:0.2167	rl:i:921840
-Pp01	47851208	152234	155151	+	chr9	23006712	13559728	13562671	66	2943	7	tp:A:P	cm:i:8	s1:i:61	s2:i:0	dv:f:0.2801	rl:i:921840
-Pp01	47851208	155693	157683	+	chr9	23006712	13564184	13566283	144	2114	28	tp:A:P	cm:i:18	s1:i:120	s2:i:0	dv:f:0.2021	rl:i:921840
-Pp01	47851208	182398	183170	-	chr9	23006712	13416305	13417077	95	772	22	tp:A:P	cm:i:11	s1:i:95	s2:i:0	dv:f:0.1728	rl:i:921840
-Pp01	47851208	190128	190583	+	chr11	19818926	13484635	13485088	52	455	4	tp:A:P	cm:i:6	s1:i:52	s2:i:0	dv:f:0.1735	rl:i:921840
-Pp01	47851208	198416	198881	+	chr11	19818926	13484635	13485088	67	465	9	tp:A:P	cm:i:7	s1:i:65	s2:i:0	dv:f:0.1664	rl:i:921840
-Pp01	47851208	200192	200573	-	chr9	23006712	13414133	13414502	69	381	10	tp:A:P	cm:i:5	s1:i:67	s2:i:0	dv:f:0.1750	rl:i:921840
-Pp01	47851208	226325	227449	-	chr11	19818926	13696059	13697131	53	1124	1	tp:A:P	cm:i:4	s1:i:44	s2:i:0	dv:f:0.2672	rl:i:921840
-Pp01	47851208	271401	271610	+	chr11	19818926	12455072	12455276	43	209	0	tp:A:P	cm:i:4	s1:i:42	s2:i:0	dv:f:0.1483	rl:i:921840
-Pp01	47851208	293468	294021	-	chr5	25021643	13433981	13434596	101	616	20	tp:A:P	cm:i:8	s1:i:90	s2:i:0	dv:f:0.1704	rl:i:921840
-Pp01	47851208	295962	296255	-	chr5	25021643	13417867	13418160	47	293	2	tp:A:P	cm:i:4	s1:i:47	s2:i:0	dv:f:0.1723	rl:i:921840
-Pp01	47851208	297240	297553	-	chr5	25021643	13409896	13410221	63	325	7	tp:A:P	cm:i:5	s1:i:61	s2:i:0	dv:f:0.1668	rl:i:921840
-Pp01	47851208	308074	310236	+	chr5	25021643	13571677	13573799	275	2162	43	tp:A:P	cm:i:27	s1:i:268	s2:i:0	dv:f:0.1797	rl:i:921840
-Pp01	47851208	336437	336584	-	chr13	24396255	11913987	11914116	44	147	0	tp:A:P	cm:i:5	s1:i:40	s2:i:0	dv:f:0.1149	rl:i:921840
-Pp01	47851208	337661	338528	+	chr5	25021643	11914299	11915296	111	998	19	tp:A:P	cm:i:9	s1:i:87	s2:i:0	dv:f:0.1947	rl:i:921840

package/src/PAFAdapter/util.test.ts

@@ -1,7 +0,0 @@
-import { flipCigar } from './util'
-
-test('flip cigar', () => {
-  expect(flipCigar(['3', 'M', '5', 'D', '5', 'M', '5', 'I', '6', 'M'])).toEqual(
-    ['6', 'M', '5', 'D', '5', 'M', '5', 'I', '3', 'M'],
-  )
-})

package/src/PAFAdapter/util.ts

@@ -1,176 +0,0 @@
-import { zip } from '../util'
-
-export interface PAFRecord {
-  qname: string
-  qstart: number
-  qend: number
-  tname: string
-  tstart: number
-  tend: number
-  strand: number
-  extra: {
-    cg?: string
-    blockLen?: number
-    mappingQual: number
-    numMatches?: number
-    meanScore?: number
-  }
-}
-// based on "weighted mean" method from https://github.com/tpoorten/dotPlotly
-// License reproduced here
-//
-// MIT License
-
-// Copyright (c) 2017 Tom Poorten
-
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-
-// The above copyright notice and this permission notice shall be included in all
-// copies or substantial portions of the Software.
-
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-//
-// Notes: in the weighted mean longer alignments factor in more heavily of all
-// the fragments of a query vs the reference that it mapped to
-//
-// this uses a combined key query+'-'+ref to iteratively map all the alignments
-// that match a particular ref from a particular query (so 1d array of what
-// could be a 2d map)
-//
-// the result is a single number that says e.g. chr5 from human mapped to chr5
-// on mouse with 0.8 quality, and that0.8 is then attached to all the pieces of
-// chr5 on human that mapped to chr5 on mouse. if chr5 on human also more
-// weakly mapped to chr6 on mouse, then it would have another value e.g. 0.6.
-// this can show strong and weak levels of synteny, especially in polyploidy
-// situations
-
-export function getWeightedMeans(ret: PAFRecord[]) {
-  const scoreMap: { [key: string]: { quals: number[]; len: number[] } } = {}
-  for (let i = 0; i < ret.length; i++) {
-    const entry = ret[i]
-    const query = entry.qname
-    const target = entry.tname
-    const key = query + '-' + target
-    if (!scoreMap[key]) {
-      scoreMap[key] = { quals: [], len: [] }
-    }
-    scoreMap[key].quals.push(entry.extra.mappingQual)
-    scoreMap[key].len.push(entry.extra.blockLen || 1)
-  }
-
-  const meanScoreMap = Object.fromEntries(
-    Object.entries(scoreMap).map(([key, val]) => {
-      const vals = zip(val.quals, val.len)
-      return [key, weightedMean(vals)]
-    }),
-  )
-  for (let i = 0; i < ret.length; i++) {
-    const entry = ret[i]
-    const query = entry.qname
-    const target = entry.tname
-    const key = query + '-' + target
-    entry.extra.meanScore = meanScoreMap[key]
-  }
-
-  let min = 10000
-  let max = 0
-  for (let i = 0; i < ret.length; i++) {
-    const entry = ret[i]
-    min = Math.min(entry.extra.meanScore || 0, min)
-    max = Math.max(entry.extra.meanScore || 0, max)
-  }
-  for (let i = 0; i < ret.length; i++) {
-    const entry = ret[i]
-    const b = entry.extra.meanScore || 0
-    entry.extra.meanScore = (b - min) / (max - min)
-  }
-
-  return ret
-}
-
-// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
-function weightedMean(tuples: [number, number][]) {
-  // eslint-disable-next-line unicorn/no-array-reduce
-  const [valueSum, weightSum] = tuples.reduce(
-    ([valueSum, weightSum], [value, weight]) => [
-      valueSum + value * weight,
-      weightSum + weight,
-    ],
-    [0, 0],
-  )
-  return valueSum / weightSum
-}
-
-export function parsePAFLine(line: string) {
-  const [
-    qname,
-    ,
-    qstart,
-    qend,
-    strand,
-    tname,
-    ,
-    tstart,
-    tend,
-    numMatches,
-    blockLen,
-    mappingQual,
-    ...fields
-  ] = line.split('\t')
-
-  const rest = Object.fromEntries(
-    fields.map(field => {
-      const r = field.indexOf(':')
-      const fieldName = field.slice(0, r)
-      const fieldValue = field.slice(r + 3)
-      return [fieldName, fieldValue]
-    }),
-  )
-
-  return {
-    tname,
-    tstart: +tstart,
-    tend: +tend,
-    qname,
-    qstart: +qstart,
-    qend: +qend,
-    strand: strand === '-' ? -1 : 1,
-    extra: {
-      numMatches: +numMatches,
-      blockLen: +blockLen,
-      mappingQual: +mappingQual,
-      ...rest,
-    },
-  } as PAFRecord
-}
-
-export function flipCigar(cigar: string[]) {
-  const arr = []
-  for (let i = cigar.length - 2; i >= 0; i -= 2) {
-    arr.push(cigar[i])
-    const op = cigar[i + 1]
-    if (op === 'D') {
-      arr.push('I')
-    } else if (op === 'I') {
-      arr.push('D')
-    } else {
-      arr.push(op)
-    }
-  }
-  return arr
-}
-
-export function swapIndelCigar(cigar: string) {
-  return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')
-}

package/src/index.ts

@@ -1,62 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { FileLocation } from '@jbrowse/core/util/types'
-
-import PAFAdapterF from './PAFAdapter'
-import MCScanAnchorsAdapterF from './MCScanAnchorsAdapter'
-import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter'
-import MashMapAdapterF from './MashMapAdapter'
-import DeltaAdapterF from './DeltaAdapter'
-import ChainAdapterF from './ChainAdapter'
-
-import {
-  getFileName,
-  AdapterGuesser,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
-
-export default class ComparativeAdaptersPlugin extends Plugin {
-  name = 'ComparativeAdaptersPlugin'
-
-  install(pluginManager: PluginManager) {
-    PAFAdapterF(pluginManager)
-    DeltaAdapterF(pluginManager)
-    ChainAdapterF(pluginManager)
-    MCScanAnchorsAdapterF(pluginManager)
-    MCScanSimpleAnchorsAdapterF(pluginManager)
-    MashMapAdapterF(pluginManager)
-
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.paf/i
-          const adapterName = 'PAFAdapter'
-          const fileName = getFileName(file)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              pafLocation: file,
-            }
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
-    pluginManager.addToExtensionPoint(
-      'Core-guessTrackTypeForLocation',
-      (trackTypeGuesser: TrackTypeGuesser) => {
-        return (adapterName: string) => {
-          if (adapterName === 'PAFAdapter') {
-            return 'SyntenyTrack'
-          }
-          return trackTypeGuesser(adapterName)
-        }
-      },
-    )
-  }
-}

package/src/util.ts

@@ -1,66 +0,0 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { GenericFilehandle } from 'generic-filehandle'
-import { unzip } from '@gmod/bgzf-filehandle'
-import { PAFRecord } from './PAFAdapter/util'
-
-export function isGzip(buf: Buffer) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
-}
-
-export function parseBed(text: string) {
-  return new Map(
-    text
-      .split(/\n|\r\n|\r/)
-      .filter(f => !!f || f.startsWith('#'))
-      .map(line => {
-        const [refName, start, end, name, score, strand] = line.split('\t')
-        return [
-          name,
-          {
-            refName,
-            start: +start,
-            end: +end,
-            score: +score,
-            name,
-            strand: strand === '-' ? -1 : 1,
-          },
-        ]
-      }),
-  )
-}
-
-export async function readFile(file: GenericFilehandle, opts?: BaseOptions) {
-  const buffer = (await file.readFile(opts)) as Buffer
-  return new TextDecoder('utf8', { fatal: true }).decode(
-    isGzip(buffer) ? await unzip(buffer) : buffer,
-  )
-}
-
-export function zip(a: number[], b: number[]) {
-  return a.map((e, i) => [e, b[i]] as [number, number])
-}
-
-const decoder =
-  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined
-
-export function parseLineByLine(
-  buffer: Buffer,
-  cb: (line: string) => PAFRecord,
-) {
-  let blockStart = 0
-  const entries = []
-  while (blockStart < buffer.length) {
-    const n = buffer.indexOf('\n', blockStart)
-    if (n === -1) {
-      break
-    }
-    const b = buffer.slice(blockStart, n)
-    const line = (decoder?.decode(b) || b.toString()).trim()
-    if (line) {
-      entries.push(cb(line))
-    }
-
-    blockStart = n + 1
-  }
-  return entries
-}