@jbrowse/plugin-comparative-adapters 2.6.1 → 2.6.3

package/esm/MCScanSimpleAnchorsAdapter/index.js.map

@@ -1 +0,0 @@
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package/esm/MashMapAdapter/MashMapAdapter.js.map

@@ -1 +0,0 @@
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package/esm/MashMapAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/esm/MashMapAdapter/index.js.map

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package/esm/PAFAdapter/PAFAdapter.js.map

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package/esm/PAFAdapter/SyntenyFeature.js.map

@@ -1 +0,0 @@
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package/esm/PAFAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/esm/PAFAdapter/index.js.map

@@ -1 +0,0 @@
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package/esm/PAFAdapter/util.js.map

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package/esm/util.js.map

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package/src/ChainAdapter/ChainAdapter.ts

@@ -1,18 +0,0 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { openLocation } from '@jbrowse/core/util/io'
-import { unzip } from '@gmod/bgzf-filehandle'
-import PAFAdapter from '../PAFAdapter/PAFAdapter'
-import { paf_chain2paf } from './util'
-
-function isGzip(buf: Buffer) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
-}
-
-export default class ChainAdapter extends PAFAdapter {
-  async setupPre(opts?: BaseOptions) {
-    const loc = openLocation(this.getConf('chainLocation'), this.pluginManager)
-    const buffer = (await loc.readFile(opts)) as Buffer
-    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
-    return paf_chain2paf(buf)
-  }
-}

package/src/ChainAdapter/configSchema.ts

@@ -1,50 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config ChainAdapter
- * #category adapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const ChainAdapter = ConfigurationSchema(
-  'ChainAdapter',
-  {
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      type: 'stringArray',
-      defaultValue: [],
-      description:
-        'Target is the first value in the array, query is the second',
-    },
-    /**
-     * #slot
-     * can be specified as alternative to assemblyNames
-     */
-    targetAssembly: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Alternative to assemblyNames array: the target assembly',
-    },
-    /**
-     * #slot
-     * can be specified as alternative to assemblyNames
-     */
-    queryAssembly: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Alternative to assemblyNames array: the query assembly',
-    },
-    /**
-     * #slot
-     */
-    chainLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/file.chain', locationType: 'UriLocation' },
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default ChainAdapter

package/src/ChainAdapter/index.ts

@@ -1,18 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'ChainAdapter',
-        displayName: 'Liftover chain adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () => import('./ChainAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/ChainAdapter/util.ts

@@ -1,170 +0,0 @@
-const decoder =
-  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined
-
-/* adapted from chain2paf by Andrea Guarracino, license reproduced below
- *
- * MIT License
- *
- * Copyright (c) 2021 Andrea Guarracino
- *
- * 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.
- */
-
-function generate_record(
-  qname: string,
-  qstart: number,
-  qend: number,
-  qstrand: string,
-  tname: string,
-  tstart: number,
-  tend: number,
-  cigar: string,
-  numMatches: number,
-) {
-  return {
-    qname,
-    qstart,
-    qend,
-    tname,
-    tstart,
-    tend,
-    strand: qstrand === '-' ? -1 : 1,
-    extra: {
-      numMatches,
-      blockLen: Math.max(qend - qstart, tend - tstart),
-      mappingQual: 0,
-      cg: cigar,
-    },
-  }
-}
-
-export function paf_chain2paf(buffer: Buffer) {
-  let t_name = ''
-  let t_start = 0
-  let t_end = 0
-  let q_name = ''
-  let q_size = ''
-  let q_strand = ''
-  let q_start = 0
-  let q_end = 0
-  let num_matches = 0
-  let cigar = ''
-  const records = []
-
-  let blockStart = 0
-  while (blockStart < buffer.length) {
-    const n = buffer.indexOf('\n', blockStart)
-    if (n === -1) {
-      break
-    }
-    const b = buffer.slice(blockStart, n)
-    const l = (decoder?.decode(b) || b.toString()).trim()
-    blockStart = n + 1
-    const l_tab = l.replaceAll(' ', '\t') // There are CHAIN files with space-separated fields
-    const l_vec = l_tab.split('\t')
-
-    if (l_vec[0] === 'chain') {
-      // Emit previous PAF row, if available
-      if (cigar) {
-        records.push(
-          generate_record(
-            q_name,
-            q_start,
-            q_end,
-            q_strand,
-            t_name,
-            t_start,
-            t_end,
-            cigar,
-            num_matches,
-          ),
-        )
-      }
-
-      // Save query/target information
-      // score -- chain score
-      // tName -- chromosome (reference sequence)
-      // tSize -- chromosome size (reference sequence)
-      // tStrand -- strand (reference sequence)
-      // tStart -- alignment start position (reference sequence)
-      // tEnd -- alignment end position (reference sequence)
-      // qName -- chromosome (query sequence)
-      // qSize -- chromosome size (query sequence)
-      // qStrand -- strand (query sequence)
-      // qStart -- alignment start position (query sequence)
-      // qEnd -- alignment end position (query sequence)
-      // id -- chain ID
-      t_name = l_vec[2]
-      t_start = +l_vec[5]
-      t_end = +l_vec[6]
-      q_name = l_vec[7]
-      q_size = l_vec[8]
-      q_strand = l_vec[9]
-      q_start = +l_vec[10]
-      q_end = +l_vec[11]
-      if (q_strand === '-') {
-        const tmp = q_start
-        q_start = +q_size - q_end
-        q_end = +q_size - tmp
-      }
-
-      // Initialize PAF fields
-      num_matches = 0
-      cigar = ''
-    } else {
-      // size -- the size of the ungapped alignment
-      //
-      // dt -- the difference between the end of this block and the beginning
-      //    of the next block (reference sequence)
-      //
-      // dq -- the difference between the end of this block and the beginning
-      //    of the next block (query sequence)
-      const size_ungapped_alignment = +l_vec[0] || 0
-      const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0
-      const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0
-
-      if (size_ungapped_alignment !== 0) {
-        num_matches += +size_ungapped_alignment
-        cigar += size_ungapped_alignment + 'M'
-      }
-      if (diff_in_query !== 0) {
-        cigar += diff_in_query + 'I'
-      }
-      if (diff_in_target !== 0) {
-        cigar += diff_in_target + 'D'
-      }
-    }
-  }
-
-  // Emit last PAF row, if available
-  if (cigar) {
-    generate_record(
-      q_name,
-      q_start,
-      q_end,
-      q_strand,
-      t_name,
-      t_start,
-      t_end,
-      cigar,
-      num_matches,
-    )
-  }
-  return records
-}

package/src/DeltaAdapter/DeltaAdapter.ts

@@ -1,18 +0,0 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { openLocation } from '@jbrowse/core/util/io'
-import { unzip } from '@gmod/bgzf-filehandle'
-import PAFAdapter from '../PAFAdapter/PAFAdapter'
-import { paf_delta2paf } from './util'
-
-function isGzip(buf: Buffer) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
-}
-
-export default class DeltaAdapter extends PAFAdapter {
-  async setupPre(opts?: BaseOptions) {
-    const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager)
-    const buffer = (await loc.readFile(opts)) as Buffer
-    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
-    return paf_delta2paf(buf)
-  }
-}

package/src/DeltaAdapter/configSchema.ts

@@ -1,50 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config DeltaAdapter
- * #category adapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const DeltaAdapter = ConfigurationSchema(
-  'DeltaAdapter',
-  {
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      type: 'stringArray',
-      defaultValue: [],
-      description:
-        'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second',
-    },
-    /**
-     * #slot
-     * alternative to assembly names
-     */
-    targetAssembly: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Alternative to assemblyNames: the target assembly name',
-    },
-    /**
-     * #slot
-     * alternative to assembly names
-     */
-    queryAssembly: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Alternative to assemblyNames: the query assembly name',
-    },
-    /**
-     * #slot
-     */
-    deltaLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/file.delta', locationType: 'UriLocation' },
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default DeltaAdapter

package/src/DeltaAdapter/index.ts

@@ -1,18 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'DeltaAdapter',
-        displayName: 'MUMmer delta adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () => import('./DeltaAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/DeltaAdapter/util.ts

@@ -1,149 +0,0 @@
-const decoder =
-  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined
-
-/* paf2delta from paftools.js in the minimap2 repository, license reproduced below
- *
- * The MIT License
- *
- * Copyright (c) 2018-     Dana-Farber Cancer Institute
- *               2017-2018 Broad Institute, Inc.
- *
- * 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.
- */
-
-export function paf_delta2paf(buffer: Buffer) {
-  let rname = ''
-  let qname = ''
-  let qs = 0
-  let qe = 0
-  let rs = 0
-  let re = 0
-  let strand = 0
-  let NM = 0
-  let cigar = [] as number[]
-  let x = 0
-  let y = 0
-  let seen_gt = false
-
-  const records = []
-  const regex = new RegExp(/^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/)
-
-  let blockStart = 0
-  let i = 0
-  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()
-    blockStart = n + 1
-    i++
-    if (line) {
-      const m = regex.exec(line)
-      if (m !== null) {
-        rname = m[1]
-        qname = m[2]
-        seen_gt = true
-        continue
-      }
-      if (!seen_gt) {
-        continue
-      }
-      const t = line.split(' ')
-      if (t.length === 7) {
-        const t0 = +t[0]
-        const t1 = +t[1]
-        const t2 = +t[2]
-        const t3 = +t[3]
-        const t4 = +t[4]
-        strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1
-        rs = +(t0 < t1 ? t0 : t1) - 1
-        re = +(t1 > t0 ? t1 : t0)
-        qs = +(t2 < t3 ? t2 : t3) - 1
-        qe = +(t3 > t2 ? t3 : t2)
-        x = y = 0
-        NM = t4
-        cigar = []
-      } else if (t.length === 1) {
-        const d = +t[0]
-        if (d === 0) {
-          let blen = 0
-          const cigar_str = []
-
-          if (re - rs - x !== qe - qs - y) {
-            throw new Error(`inconsistent alignment on line ${i}`)
-          }
-          cigar.push((re - rs - x) << 4)
-          for (let i = 0; i < cigar.length; ++i) {
-            const rlen = cigar[i] >> 4
-            blen += rlen
-            cigar_str.push(rlen + 'MID'.charAt(cigar[i] & 0xf))
-          }
-
-          records.push({
-            qname,
-            qstart: qs,
-            qend: qe,
-            tname: rname,
-            tstart: rs,
-            tend: re,
-            strand,
-            extra: {
-              numMatches: blen - NM,
-              blockLen: blen,
-              mappingQual: 0,
-              NM,
-              cg: cigar_str.join(''),
-            },
-          })
-        } else if (d > 0) {
-          const l = d - 1
-          x += l + 1
-          y += l
-          if (l > 0) {
-            cigar.push(l << 4)
-          }
-          // eslint-disable-next-line unicorn/prefer-at
-          if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
-            cigar[cigar.length - 1] += 1 << 4
-          } else {
-            cigar.push((1 << 4) | 2)
-          } // deletion
-        } else {
-          const l = -d - 1
-          x += l
-          y += l + 1
-          if (l > 0) {
-            cigar.push(l << 4)
-          }
-          // eslint-disable-next-line unicorn/prefer-at
-          if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
-            cigar[cigar.length - 1] += 1 << 4
-          } else {
-            cigar.push((1 << 4) | 1)
-          } // insertion
-        }
-      }
-    }
-  }
-  return records
-}

package/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.test.ts

@@ -1,45 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './MCScanAnchorsAdapter'
-
-import configSchema from './configSchema'
-
-test('adapter can fetch features from mcscan anchors file', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      mcscanAnchorsLocation: {
-        localPath: require.resolve('./test_data/grape.peach.anchors.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      bed1Location: {
-        localPath: require.resolve('./test_data/grape.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      bed2Location: {
-        localPath: require.resolve('./test_data/peach.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-
-      assemblyNames: ['grape', 'peach'],
-    }),
-  )
-
-  const features1 = adapter.getFeatures({
-    refName: 'Pp01',
-    start: 0,
-    end: 200000,
-    assemblyName: 'peach',
-  })
-
-  const features2 = adapter.getFeatures({
-    refName: 'chr1',
-    start: 0,
-    end: 200000,
-    assemblyName: 'grape',
-  })
-
-  const fa1 = await firstValueFrom(features1.pipe(toArray()))
-  const fa2 = await firstValueFrom(features2.pipe(toArray()))
-  expect(fa1.length).toBe(7)
-  expect(fa2.length).toBe(8)
-})