Add new coloring options for dotplot and ability to "rectangularize" …

…dotplot view (#2791)

* Dotplot mods

* Updates

* Draw open circles for large CIGAR

* Remove ctrl+scroll in dotplot

* Misc

* Add method to only connect indels of a certain size

* Add a br breakpoint in dotplot header

* Add dotplot renderer line width

* Fix lint

* Put target assembly on x-axis for dotplot

* Color by qual

* Line width 2.5

* Re-organize paf record

* Update comment

* Thresholds config editing

* Less circles

* Create MashMap adapter, since mashmap doesn't follow the format of paf
after col 9, this let's us load score more reliably

* Remove large indel limit

* Back to main

* Code simplify

* Add ability to load MCScan .anchors and .anchors.simple files using the GUI import forms for dotplot/synteny views (#2792)


* Update mcscan anchors adapter to take a bed1Location and bed2Location

* Standardize on left and right columns for mcscan anchors

* Improve anchors importing

* Add simple anchors example

* Add simple anchors to import form

* Update mcscan synteny config

* Add delta example to grape vs peach dotplot

* T1

* Unify simpleanchors and anchors somewhat

packages/core/util/index.ts

@@ -1121,3 +1121,15 @@ export function viewBpToPx({
 
   return undefined
 }
+
+export function getBpDisplayStr(totalBp: number) {
+  let displayBp
+  if (Math.floor(totalBp / 1000000) > 0) {
+    displayBp = `${parseFloat((totalBp / 1000000).toPrecision(3))}Mbp`
+  } else if (Math.floor(totalBp / 1000) > 0) {
+    displayBp = `${parseFloat((totalBp / 1000).toPrecision(3))}Kbp`
+  } else {
+    displayBp = `${Math.floor(totalBp)}bp`
+  }
+  return displayBp
+}

plugins/comparative-adapters/src/ChainAdapter/ChainAdapter.ts

@@ -1,20 +1,8 @@
 import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { readConfObject } from '@jbrowse/core/configuration'
 import { unzip } from '@gmod/bgzf-filehandle'
 import PAFAdapter from '../PAFAdapter/PAFAdapter'
 
-interface PafRecord {
-  records: NoAssemblyRegion[]
-  extra: {
-    blockLen: number
-    mappingQual: number
-    numMatches: number
-    strand: number
-  }
-}
-
 function isGzip(buf: Buffer) {
   return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
 }
@@ -45,29 +33,31 @@ function isGzip(buf: Buffer) {
  */
 
 function generate_record(
-  q_name: string,
-  q_start: number,
-  q_end: number,
-  q_strand: string,
-  t_name: string,
-  t_start: number,
-  t_end: number,
+  qname: string,
+  qstart: number,
+  qend: number,
+  qstrand: string,
+  tname: string,
+  tstart: number,
+  tend: number,
   cigar: string,
-  num_matches: number,
+  numMatches: number,
 ) {
   return {
-    records: [
-      { refName: q_name, start: q_start, end: q_end },
-      { refName: t_name, start: t_start, end: t_end },
-    ],
+    qname,
+    qstart,
+    qend,
+    tname,
+    tstart,
+    tend,
+    strand: qstrand === '-' ? -1 : 1,
     extra: {
-      numMatches: num_matches,
-      blockLen: Math.max(q_end - q_start, t_end - t_start),
-      strand: q_strand === '-' ? -1 : 1,
+      numMatches,
+      blockLen: Math.max(qend - qstart, tend - tstart),
       mappingQual: 0,
       cg: cigar,
     },
-  } as PafRecord
+  }
 }
 
 function paf_chain2paf(lines: string[]) {
@@ -179,11 +169,8 @@ function paf_chain2paf(lines: string[]) {
 
 export default class ChainAdapter extends PAFAdapter {
   async setupPre(opts?: BaseOptions) {
-    const chainLocation = openLocation(
-      readConfObject(this.config, 'chainLocation'),
-      this.pluginManager,
-    )
-    const buffer = (await chainLocation.readFile(opts)) as Buffer
+    const loc = openLocation(this.getConf('chainLocation'), this.pluginManager)
+    const buffer = (await loc.readFile(opts)) as Buffer
     const buf = isGzip(buffer) ? await unzip(buffer) : buffer
     // 512MB  max chrome string length is 512MB
     if (buf.length > 536_870_888) {

plugins/comparative-adapters/src/ChainAdapter/configSchema.ts

@@ -6,6 +6,18 @@ export default ConfigurationSchema(
     assemblyNames: {
       type: 'stringArray',
       defaultValue: [],
+      description:
+        'Target is the first value in the array, query is the second',
+    },
+    targetAssembly: {
+      type: 'string',
+      defaultValue: '',
+      description: 'Alternative to assemblyNames array: the target assembly',
+    },
+    queryAssembly: {
+      type: 'string',
+      defaultValue: '',
+      description: 'Alternative to assemblyNames array: the query assembly',
     },
     chainLocation: {
       type: 'fileLocation',

plugins/comparative-adapters/src/DeltaAdapter/DeltaAdapter.ts

@@ -1,20 +1,8 @@
 import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { readConfObject } from '@jbrowse/core/configuration'
 import { unzip } from '@gmod/bgzf-filehandle'
 import PAFAdapter from '../PAFAdapter/PAFAdapter'
 
-interface PafRecord {
-  records: NoAssemblyRegion[]
-  extra: {
-    blockLen: number
-    mappingQual: number
-    numMatches: number
-    strand: number
-  }
-}
-
 function isGzip(buf: Buffer) {
   return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
 }
@@ -101,24 +89,27 @@ function paf_delta2paf(lines: string[]) {
         }
         cigar.push((re - rs - x) << 4)
         for (let i = 0; i < cigar.length; ++i) {
-          blen += cigar[i] >> 4
-          cigar_str.push((cigar[i] >> 4) + 'MID'.charAt(cigar[i] & 0xf))
+          const rlen = cigar[i] >> 4
+          blen += rlen
+          cigar_str.push(rlen + 'MID'.charAt(cigar[i] & 0xf))
         }
 
         records.push({
-          records: [
-            { refName: qname, start: qs, end: qe },
-            { refName: rname, start: rs, end: re },
-          ],
+          qname,
+          qstart: qs,
+          qend: qe,
+          tname: rname,
+          tstart: rs,
+          tend: re,
+          strand,
           extra: {
             numMatches: blen - NM,
             blockLen: blen,
-            strand,
             mappingQual: 0,
             NM,
             cg: cigar_str.join(''),
           },
-        } as PafRecord)
+        })
       } else if (d > 0) {
         const l = d - 1
         x += l + 1
@@ -151,11 +142,8 @@ function paf_delta2paf(lines: string[]) {
 
 export default class DeltaAdapter extends PAFAdapter {
   async setupPre(opts?: BaseOptions) {
-    const deltaLocation = openLocation(
-      readConfObject(this.config, 'deltaLocation'),
-      this.pluginManager,
-    )
-    const buffer = (await deltaLocation.readFile(opts)) as Buffer
+    const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager)
+    const buffer = (await loc.readFile(opts)) as Buffer
     const buf = isGzip(buffer) ? await unzip(buffer) : buffer
     // 512MB  max chrome string length is 512MB
     if (buf.length > 536_870_888) {

plugins/comparative-adapters/src/DeltaAdapter/configSchema.ts

@@ -6,6 +6,18 @@ export default ConfigurationSchema(
     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',
+    },
+    targetAssembly: {
+      type: 'string',
+      defaultValue: '',
+      description: 'Alternative to assemblyNames: the target assembly name',
+    },
+    queryAssembly: {
+      type: 'string',
+      defaultValue: '',
+      description: 'Alternative to assemblyNames: the query assembly name',
     },
     deltaLocation: {
       type: 'fileLocation',

plugins/comparative-adapters/src/MCScanAnchorsAdapter/MCScanAnchorsAdapter.test.ts

@@ -1,10 +1,4 @@
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { Region } from '@jbrowse/core/util/types'
 import { toArray } from 'rxjs/operators'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { ConfigurationSchema } from '@jbrowse/core/configuration/configurationSchema'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import Adapter from './MCScanAnchorsAdapter'
 import { TextEncoder, TextDecoder } from 'web-encoding'
 import configSchema from './configSchema'
@@ -16,85 +10,42 @@ if (!window.TextDecoder) {
   window.TextDecoder = TextDecoder
 }
 
-class CustomAdapter extends BaseFeatureDataAdapter {
-  async getRefNames() {
-    return []
-  }
-
-  freeResources() {}
-
-  getFeatures(region: Region) {
-    return ObservableCreate<Feature>(async observer => {
-      if (region.assemblyName === 'peach') {
-        observer.next(
-          new SimpleFeature({
-            uniqueId: '1',
-            start: 0,
-            end: 100,
-            refName: 'peach_chr1',
-            syntenyId: 1,
-            name: 'GSVIVT01012253001',
-          }),
-        )
-      }
-      if (region.assemblyName === 'grape') {
-        observer.next(
-          new SimpleFeature({
-            start: 0,
-            uniqueId: '2',
-            end: 100,
-            refName: 'grape_chr1',
-            syntenyId: 1,
-            name: 'Prupe.1G290800.1',
-          }),
-        )
-      }
-      observer.complete()
-    })
-  }
-}
-
-const getSubAdapter: getSubAdapterType = async () => {
-  return {
-    dataAdapter: new CustomAdapter(ConfigurationSchema('empty', {}).create()),
-    sessionIds: new Set(),
-  }
-}
-test('adapter can fetch features from volvox.bam', async () => {
+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'),
+        localPath: require.resolve('./test_data/grape.peach.anchors.gz'),
         locationType: 'LocalPathLocation',
       },
-      subadapters: [
-        ConfigurationSchema('empty', {}).create(),
-        ConfigurationSchema('empty', {}).create(),
-      ],
+      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'],
     }),
-    getSubAdapter,
   )
 
   const features1 = adapter.getFeatures({
-    refName: 'peach_chr1',
+    refName: 'Pp01',
     start: 0,
-    end: 20000,
+    end: 200000,
     assemblyName: 'peach',
   })
 
   const features2 = adapter.getFeatures({
-    refName: 'grape_chr1',
+    refName: 'chr1',
     start: 0,
-    end: 20000,
+    end: 200000,
     assemblyName: 'grape',
   })
 
   const fa1 = await features1.pipe(toArray()).toPromise()
   const fa2 = await features2.pipe(toArray()).toPromise()
-  expect(fa1.length).toBe(2)
-  expect(fa2.length).toBe(1)
-  expect(fa1[0].get('refName')).toBe('peach_chr1')
-  expect(fa2[0].get('refName')).toBe('grape_chr1')
-  expect(fa1[0].get('syntenyId')).toEqual(fa2[0].get('syntenyId'))
+  expect(fa1.length).toBe(7)
+  expect(fa2.length).toBe(8)
 })