@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/src/{LinearPileupDisplay/components → shared}/FilterByTag.tsx

@@ -2,31 +2,21 @@ import React, { useState } from 'react'
 import { observer } from 'mobx-react'
 import {
   Button,
-  Dialog,
   DialogActions,
   DialogContent,
-  DialogTitle,
-  IconButton,
   Link,
   Paper,
   TextField,
   Typography,
 } from '@mui/material'
+import { Dialog } from '@jbrowse/core/ui'
 import { makeStyles } from 'tss-react/mui'
 
-import CloseIcon from '@mui/icons-material/Close'
-
 const useStyles = makeStyles()(theme => ({
   paper: {
     padding: theme.spacing(2),
     margin: theme.spacing(2),
   },
-  closeButton: {
-    position: 'absolute',
-    right: theme.spacing(1),
-    top: theme.spacing(1),
-    color: theme.palette.grey[500],
-  },
   field: {
     margin: theme.spacing(2),
   },
@@ -105,17 +95,7 @@ function FilterByTagDlg(props: {
   const site = 'https://broadinstitute.github.io/picard/explain-flags.html'
 
   return (
-    <Dialog open onClose={handleClose}>
-      <DialogTitle>
-        Filter options
-        <IconButton
-          aria-label="close"
-          className={classes.closeButton}
-          onClick={handleClose}
-        >
-          <CloseIcon />
-        </IconButton>
-      </DialogTitle>
+    <Dialog open onClose={handleClose} title="Filter options">
       <DialogContent>
         <Typography>
           Set filter bitmask options. Refer to <Link href={site}>{site}</Link>{' '}
@@ -143,9 +123,7 @@ function FilterByTagDlg(props: {
           <TextField
             className={classes.field}
             value={tag}
-            onChange={event => {
-              setTag(event.target.value)
-            }}
+            onChange={event => setTag(event.target.value)}
             placeholder="Enter tag name"
             inputProps={{
               maxLength: 2,
@@ -158,9 +136,7 @@ function FilterByTagDlg(props: {
           <TextField
             className={classes.field}
             value={tagValue}
-            onChange={event => {
-              setTagValue(event.target.value)
-            }}
+            onChange={event => setTagValue(event.target.value)}
             placeholder="Enter tag value"
             inputProps={{
               'data-testid': 'color-tag-name-input',
@@ -173,9 +149,7 @@ function FilterByTagDlg(props: {
           <TextField
             className={classes.field}
             value={readName}
-            onChange={event => {
-              setReadName(event.target.value)
-            }}
+            onChange={event => setReadName(event.target.value)}
             placeholder="Enter read name"
             inputProps={{
               'data-testid': 'color-tag-readname-input',

package/src/shared/color.ts

@@ -0,0 +1,47 @@
+import { orientationTypes } from '../util'
+import { ChainStats } from './fetchChains'
+
+const alignmentColoring: { [key: string]: string } = {
+  color_pair_lr: '#c8c8c8',
+  color_pair_rr: 'navy',
+  color_pair_rl: 'teal',
+  color_pair_ll: 'green',
+}
+
+export function getInsertSizeColor(
+  f1: { refName: string; tlen?: number },
+  f2: { refName: string },
+  stats?: ChainStats,
+) {
+  const sameRef = f1.refName === f2.refName
+  const tlen = Math.abs(f1.tlen || 0)
+  if (sameRef && tlen > (stats?.upper || 0)) {
+    return 'red'
+  } else if (sameRef && tlen < (stats?.lower || 0)) {
+    return '#f0f'
+  } else if (!sameRef) {
+    return 'purple'
+  }
+  return ''
+}
+
+export function getInsertSizeAndOrientationColor(
+  f1: { refName: string; pair_orientation?: string; tlen?: number },
+  f2: { refName: string },
+  stats?: ChainStats,
+) {
+  return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1)
+}
+
+export function getOrientationColor(f: { pair_orientation?: string }) {
+  const type = orientationTypes['fr']
+  const orientation = type[f.pair_orientation || '']
+  const map = {
+    LR: 'color_pair_lr',
+    RR: 'color_pair_rr',
+    RL: 'color_pair_rl',
+    LL: 'color_pair_ll',
+  }
+  const val = map[orientation as keyof typeof map]
+  return alignmentColoring[val] || 'grey'
+}

package/src/shared/fetchChains.ts

@@ -0,0 +1,63 @@
+import {
+  getContainingTrack,
+  getContainingView,
+  getSession,
+} from '@jbrowse/core/util'
+import { getSnapshot, IAnyStateTreeNode } from 'mobx-state-tree'
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
+type LGV = LinearGenomeViewModel
+
+export interface ReducedFeature {
+  name: string
+  strand: number
+  refName: string
+  start: number
+  end: number
+  id: string
+  flags: number
+  tlen: number
+  pair_orientation: string
+  next_ref?: string
+  next_pos?: number
+  clipPos: number
+  SA?: string
+}
+
+export interface ChainStats {
+  max: number
+  min: number
+  upper: number
+  lower: number
+}
+
+export interface ChainData {
+  chains: ReducedFeature[][]
+  stats?: ChainStats
+}
+
+export async function fetchChains(self: IAnyStateTreeNode) {
+  try {
+    const { rpcSessionId: sessionId } = getContainingTrack(self)
+    const { rpcManager } = getSession(self)
+    const view = getContainingView(self) as LGV
+
+    if (!view.initialized || self.error) {
+      return
+    }
+    self.setLoading(true)
+
+    const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
+      sessionId,
+      regions: view.staticBlocks.contentBlocks,
+      filterBy: getSnapshot(self.filterBy),
+      adapterConfig: self.adapterConfig,
+    })) as ChainData
+
+    self.setChainData(ret)
+    self.setLoading(false)
+  } catch (e) {
+    console.error(e)
+    self.setError(e)
+  }
+}

package/src/{shared.ts → shared/index.ts}

@@ -1,9 +1,8 @@
+import { types, IAnyStateTreeNode } from 'mobx-state-tree'
 import { BlockSet } from '@jbrowse/core/util/blockTypes'
-
 import { getSession } from '@jbrowse/core/util'
 import { getRpcSessionId } from '@jbrowse/core/util/tracks'
-import { IAnyStateTreeNode } from 'mobx-state-tree'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 
 export async function getUniqueTagValues(
   self: IAnyStateTreeNode & { adapterConfig: AnyConfigurationModel },
@@ -32,9 +31,11 @@ export async function getUniqueTagValues(
   return values as string[]
 }
 
+type Track = IAnyStateTreeNode & { configuration: AnyConfigurationModel }
+
 export async function getUniqueModificationValues(
   self: IAnyStateTreeNode & {
-    parentTrack: IAnyStateTreeNode & { configuration: AnyConfigurationModel }
+    parentTrack: Track
   },
   adapterConfig: AnyConfigurationModel,
   colorScheme: { type: string; tag?: string },
@@ -60,3 +61,15 @@ export async function getUniqueModificationValues(
   )
   return values as string[]
 }
+
+export const FilterModel = types.model({
+  flagInclude: types.optional(types.number, 0),
+  flagExclude: types.optional(types.number, 1540),
+  readName: types.maybe(types.string),
+  tagFilter: types.maybe(
+    types.model({
+      tag: types.string,
+      value: types.string,
+    }),
+  ),
+})

package/dist/BamAdapter/MismatchParser.js.map

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package/dist/LinearPileupDisplay/components/FilterByTag.js.map

@@ -1 +0,0 @@
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package/dist/shared.d.ts

@@ -1,25 +0,0 @@
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
-    adapterConfig: AnyConfigurationModel;
-}, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
-export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
-    parentTrack: IAnyStateTreeNode & {
-        configuration: AnyConfigurationModel;
-    };
-}, adapterConfig: AnyConfigurationModel, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;

package/dist/shared.js.map

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

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package/esm/LinearPileupDisplay/components/FilterByTag.js.map

@@ -1 +0,0 @@
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package/esm/shared.d.ts

@@ -1,25 +0,0 @@
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
-    adapterConfig: AnyConfigurationModel;
-}, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
-export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
-    parentTrack: IAnyStateTreeNode & {
-        configuration: AnyConfigurationModel;
-    };
-}, adapterConfig: AnyConfigurationModel, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;

package/esm/shared.js.map

@@ -1 +0,0 @@
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