jbrowse-plugin-mafviewer 1.5.0 → 1.6.0

package/README.md

@@ -2,25 +2,32 @@
 
 A viewer for multiple alignment format (MAF) files in JBrowse 2
 
-This is a port of the JBrowse 1 plugin https://github.com/cmdcolin/mafviewer to
-JBrowse 2
-
 ![](img/1.png)
 
 ## Demo
 
 https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fmaf%2Fhg38%2Fdistconfig.json&session=share-bJXbDiWcc9&password=87GhV
 
+## Supported formats
+
+This plugin supports three input formats:
+
+1. **BigMaf** - UCSC BigMaf format e.g. .bb/.bigMaf
+   (https://genome.ucsc.edu/goldenpath/help/bigMaf.html)
+2. **MAF tabix** - bgzip-compressed MAF converted to BED format with tabix index
+3. **TAF (Taffy)** - bgzip-compressed TAF format
+   (https://github.com/ComparativeGenomicsToolkit/taffy)
+
 ## GUI usage (e.g. in JBrowse Desktop)
 
 This short screenshot workflow shows how you can load your own custom MAF files
-via the GUI
+via the GUI.
 
-First install the plugin via the plugin store
+First install the plugin via the plugin store:
 
 ![](img/3.png)
 
-Then use the custom "Add track workflow"
+Then use the custom "Add track workflow":
 
 ![](img/2.png)
 
@@ -33,15 +40,45 @@ Then use the custom "Add track workflow"
   "plugins": [
     {
       "name": "MafViewer",
-      "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
+      "url": "https://jbrowse.org/plugins/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
     }
   ]
 }
 ```
 
+### Example BgzipTaffyAdapter config (TAF format)
+
+TAF (Transposed Alignment Format) is often more compact than MAF and works well
+with large multi-species alignments. See
+https://github.com/ComparativeGenomicsToolkit/taffy for more details.
+
+```json
+{
+  "type": "MafTrack",
+  "trackId": "taf-example",
+  "name": "TAF alignment",
+  "assemblyNames": ["hg38"],
+  "adapter": {
+    "type": "BgzipTaffyAdapter",
+    "tafGzLocation": {
+      "uri": "alignment.taf.gz"
+    },
+    "taiLocation": {
+      "uri": "alignment.taf.gz.tai"
+    },
+    "nhLocation": {
+      "uri": "species_tree.nh"
+    }
+  }
+}
+```
+
+The `nhLocation` is optional but provides a species tree for display in the
+sidebar.
+
 ### Example MafTabixAdapter config
 
-can use nhLocation or samples array on adapter
+You can use `nhLocation` (newick tree) or `samples` array on the adapter.
 
 ```json
 {
@@ -66,7 +103,7 @@ can use nhLocation or samples array on adapter
 
 ### Example BigMafAdapter config
 
-can use nhLocation or samples array on adapter
+You can use `nhLocation` (newick tree) or `samples` array on the adapter.
 
 ```json
 {
@@ -148,22 +185,23 @@ This page discusses some examples
 https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#maf-export
 
 Thanks to Sam Talbot (https://github.com/SamCT) for initially creating the
-Cactus -> JBrowse 2 MAF example
+Cactus -> JBrowse 2 MAF example.
 
-Please note that MAFViewer wants non-overlapping blocks, please check if this is
-the case
+Note: This plugin expects non-overlapping alignment blocks. Ensure your MAF/TAF
+file meets this requirement.
 
 ## Prepare data
 
-1. BigMaf format, which can be created following UCSC guidelines
-   (https://genome.ucsc.edu/FAQ/FAQformat.html#format9.3)
+Three formats are supported:
 
-2. MAF tabix based format, based on a custom BED created via conversion tools in
-   this repo (see maf2bed)
+1. **BigMaf** - UCSC BigMaf format (see
+   https://genome.ucsc.edu/FAQ/FAQformat.html#format9.3)
+2. **MAF tabix** - bgzip-compressed BED converted from MAF using maf2bed
+3. **TAF (Taffy)** - bgzip-compressed TAF with .tai index (recommended for large
+   alignments)
 
-_Note: All these formats generally start with a MAF as input. Note that your MAF
-file should contain the species name and chromosome name e.g. hg38.chr1 in the
-sequence identifiers._
+_Note: All formats start with a MAF as input. Your MAF file should contain the
+species name and chromosome name (e.g. hg38.chr1) in the sequence identifiers._
 
 ### Option 1. Preparing BigMaf
 
@@ -186,8 +224,8 @@ identifiers in the MAF file will say something like hg38.chr1, therefore, the
 argument to maf2bed should just be hg38 to remove hg38 part of the identifier.
 
 If your MAF file does not include the species name as part of the identifier,
-you should add the species into them the those scaffold/chromosome e.g. create
-hg38.chr1 if it was just chr1 before)
+you should add the species name to the scaffold/chromosome names (e.g. create
+hg38.chr1 if it was just chr1 before).
 
 If all is well, your BED file should have 6 columns, with
 `chr, start, end, id, score, alignment_data`, where `alignment_data` is
@@ -196,3 +234,33 @@ separated by `:`.
 
 Note: If you can't use the `cargo install maf2bed` binary, there is a
 `bin/maf2bed.pl` perl version of it in this repo
+
+### Option 3. Preparing TAF (Taffy)
+
+TAF (Transposed Alignment Format) is a column-oriented format that is often more
+compact than MAF, especially for large multi-species alignments. It uses
+run-length encoding and avoids the block fragmentation issues that MAF has with
+many sequences.
+
+Install taffy from https://github.com/ComparativeGenomicsToolkit/taffy
+
+```bash
+# Convert MAF to bgzip-compressed TAF and create index
+taffy view -i file.maf | bgzip > out.taf.gz
+taffy index -i out.taf.gz
+```
+
+This creates `out.taf.gz` and `out.taf.gz.tai` (the index file).
+
+For large alignments, you may want to normalize the TAF file first to merge
+short alignment blocks:
+
+```bash
+taffy view -i file.maf | taffy norm | bgzip > out.taf.gz
+taffy index -i out.taf.gz
+```
+
+## Footnote
+
+This is a port of the JBrowse 1 plugin https://github.com/cmdcolin/mafviewer to
+JBrowse 2

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts

@@ -2,6 +2,7 @@ import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters
 import { Feature, Region } from '@jbrowse/core/util';
 import type { RowInstruction } from './rowInstructions';
 import type { AlignmentRecord, IndexData } from './types';
+import type { MafAdapterOptions } from '../types';
 interface RowState {
     sequenceName: string;
     start: number;
@@ -26,22 +27,28 @@ interface TafFeature {
     alignments: Record<string, AlignmentRecord>;
     seq: string;
 }
+/**
+ * Adapter for TAF (Taffy Alignment Format) files compressed with BGZIP
+ * Implements streaming parsing of TAF blocks into MAF features
+ *
+ * TAF Format: https://github.com/ComparativeGenomicsToolkit/taffy
+ */
 export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     setupP?: Promise<SetupData>;
     getRefNames(): Promise<string[]>;
     parseCoordinatesAndEstablishBlock(pBlock: AlignmentBlock | undefined, instructions: RowInstruction[]): AlignmentBlock;
     parseBases(basesStr: string, runLengthEncodeBases: boolean): string;
-    parseTafBlocksStreaming(buffer: Uint8Array, runLengthEncodeBases: boolean): Generator<TafFeature>;
-    parseTafBlocks(buffer: Uint8Array, runLengthEncodeBases: boolean, _opts?: BaseOptions): TafFeature[];
+    parseTafBlocksStreaming(buffer: Uint8Array, runLengthEncodeBases: boolean, sampleFilter?: Set<string>): Generator<TafFeature>;
+    parseTafBlocks(buffer: Uint8Array, runLengthEncodeBases: boolean, _opts?: BaseOptions, sampleFilter?: Set<string>): TafFeature[];
     private decoder;
     finalizeBlock(block: AlignmentBlock, columns: string[]): void;
-    blockToFeature(block: AlignmentBlock): TafFeature | undefined;
+    blockToFeature(block: AlignmentBlock, sampleFilter?: Set<string>): TafFeature | undefined;
     setupPre(): Promise<SetupData>;
     setup(opts?: BaseOptions): Promise<SetupData>;
     doSetup(): Promise<SetupData>;
     readHeader(): Promise<boolean>;
     readTaiFile(): Promise<IndexData>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getFeatures(query: Region, opts?: MafAdapterOptions): import("rxjs").Observable<Feature>;
     getSamples(_query: Region): Promise<{
         samples: {
             id: string;

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js

@@ -4,12 +4,13 @@ import { updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import VirtualOffset from './virtualOffset';
-import parseNewick from '../parseNewick';
-import { normalize } from '../util';
 import { filterFirstLineInstructions, parseRowInstructions, } from './rowInstructions';
 import MafFeature from '../MafFeature';
 import { parseAssemblyAndChrSimple } from '../util/parseAssemblyName';
-// Binary search to find the index of the first element >= target
+import { getSamplesFromConfig } from '../util/getSamples';
+/**
+ * Binary search to find the index of the first element >= target
+ */
 function lowerBound(arr, target, getKey) {
     let lo = 0;
     let hi = arr.length;
@@ -24,6 +25,12 @@ function lowerBound(arr, target, getKey) {
     }
     return lo;
 }
+/**
+ * Adapter for TAF (Taffy Alignment Format) files compressed with BGZIP
+ * Implements streaming parsing of TAF blocks into MAF features
+ *
+ * TAF Format: https://github.com/ComparativeGenomicsToolkit/taffy
+ */
 export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     setupP;
     async getRefNames() {
@@ -108,7 +115,7 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     }
     // Streaming generator version of parseTafBlocks
     // Yields features one at a time instead of collecting into array
-    *parseTafBlocksStreaming(buffer, runLengthEncodeBases) {
+    *parseTafBlocksStreaming(buffer, runLengthEncodeBases, sampleFilter) {
         let pBlock;
         let currentBlock;
         let columns = [];
@@ -127,7 +134,7 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
                 // If we have a current block with columns, finalize and yield it
                 if (currentBlock && columns.length > 0) {
                     this.finalizeBlock(currentBlock, columns);
-                    const feature = this.blockToFeature(currentBlock);
+                    const feature = this.blockToFeature(currentBlock, sampleFilter);
                     if (feature) {
                         yield feature;
                     }
@@ -168,15 +175,17 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
         // Finalize and yield last block
         if (currentBlock && columns.length > 0) {
             this.finalizeBlock(currentBlock, columns);
-            const feature = this.blockToFeature(currentBlock);
+            const feature = this.blockToFeature(currentBlock, sampleFilter);
             if (feature) {
                 yield feature;
             }
         }
     }
     // Non-streaming version for backward compatibility (used in tests)
-    parseTafBlocks(buffer, runLengthEncodeBases, _opts) {
-        return [...this.parseTafBlocksStreaming(buffer, runLengthEncodeBases)];
+    parseTafBlocks(buffer, runLengthEncodeBases, _opts, sampleFilter) {
+        return [
+            ...this.parseTafBlocksStreaming(buffer, runLengthEncodeBases, sampleFilter),
+        ];
     }
     // TextDecoder for efficient string building from typed array
     decoder = new TextDecoder('ascii');
@@ -202,7 +211,7 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
             row.length = length;
         }
     }
-    blockToFeature(block) {
+    blockToFeature(block, sampleFilter) {
         if (block.rows.length === 0 || block.columnNumber === 0) {
             return undefined;
         }
@@ -210,6 +219,9 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
         const alignments = {};
         for (const row of block.rows) {
             const { assemblyName, chr } = parseAssemblyAndChrSimple(row.sequenceName);
+            if (sampleFilter && !sampleFilter.has(assemblyName)) {
+                continue;
+            }
             alignments[assemblyName] = {
                 chr,
                 start: row.start,
@@ -303,6 +315,9 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             try {
                 const { index, runLengthEncodeBases } = await this.setup(opts);
+                const sampleFilter = opts?.samples
+                    ? new Set(opts.samples.map(s => s.id))
+                    : undefined;
                 // Get byte range for this query
                 const records = index[query.refName];
                 if (!records || records.length === 0) {
@@ -335,7 +350,7 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
                     : buffer.length;
                 const slice = buffer.slice(startOffset, endOffset);
                 // Stream features using generator - no caching, immediate GC eligible
-                for (const feat of this.parseTafBlocksStreaming(slice, runLengthEncodeBases)) {
+                for (const feat of this.parseTafBlocksStreaming(slice, runLengthEncodeBases, sampleFilter)) {
                     // Filter features that overlap with query region
                     if (feat.end > query.start && feat.start < query.end) {
                         observer.next(new MafFeature(feat.uniqueId, feat.start, feat.end, query.refName, feat.strand, feat.alignments, feat.seq));
@@ -350,14 +365,7 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
         });
     }
     async getSamples(_query) {
-        const nhLoc = this.getConf('nhLocation');
-        const nh = nhLoc.uri === '/path/to/my.nh'
-            ? undefined
-            : await openLocation(nhLoc).readFile('utf8');
-        return {
-            samples: normalize(this.getConf('samples')),
-            tree: nh ? parseNewick(nh) : undefined,
-        };
+        return getSamplesFromConfig(this.getConf.bind(this));
     }
     freeResources() { }
 }

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js.map

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package/dist/BgzipTaffyAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
      */
@@ -40,5 +40,5 @@ declare const configSchema: import("@jbrowse/core/esm/configuration/configuratio
             locationType: string;
         };
     };
-}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/BgzipTaffyAdapter/rowInstructions.d.ts

@@ -1,3 +1,14 @@
+/**
+ * TAF (Taffy Alignment Format) row instruction types
+ * Reference: https://github.com/ComparativeGenomicsToolkit/taffy
+ *
+ * Instruction types:
+ * 'i' - insert: add a new sequence row
+ * 's' - substitute: replace coordinates of an existing row
+ * 'd' - delete: remove a sequence row
+ * 'g' - gap: add a fixed-length gap to sequence start
+ * 'G' - gap substring: add variable-length gap from substring
+ */
 interface RowInsert {
     type: 'i';
     row: number;
@@ -30,5 +41,9 @@ interface RowGapSubstring {
 }
 export type RowInstruction = RowInsert | RowDelete | RowGap | RowGapSubstring | RowSubstitute;
 export declare function filterFirstLineInstructions(instructions: RowInstruction[]): RowInstruction[];
+/**
+ * Parses TAF row instruction string into structured RowInstruction objects
+ * Each instruction token sequence is parsed according to TAF format rules
+ */
 export declare function parseRowInstructions(meta: string): RowInstruction[];
 export {};

package/dist/BgzipTaffyAdapter/rowInstructions.js

@@ -1,3 +1,14 @@
+/**
+ * TAF (Taffy Alignment Format) row instruction types
+ * Reference: https://github.com/ComparativeGenomicsToolkit/taffy
+ *
+ * Instruction types:
+ * 'i' - insert: add a new sequence row
+ * 's' - substitute: replace coordinates of an existing row
+ * 'd' - delete: remove a sequence row
+ * 'g' - gap: add a fixed-length gap to sequence start
+ * 'G' - gap substring: add variable-length gap from substring
+ */
 // Faithfully replicates change_s_coordinates_to_i from taffy/impl/tai.c
 // When starting from an indexed position:
 // 1. Convert 's' (substitute) to 'i' (insert) - because there's no previous row to substitute
@@ -20,30 +31,20 @@ export function filterFirstLineInstructions(instructions) {
         return ins;
     });
 }
+/**
+ * Parses TAF row instruction string into structured RowInstruction objects
+ * Each instruction token sequence is parsed according to TAF format rules
+ */
 export function parseRowInstructions(meta) {
     const ret = meta.split(' ');
     const rows = [];
     for (let i = 0; i < ret.length;) {
         const type = ret[i++];
-        if (type === 'i') {
-            const row = +ret[i++];
-            const sequenceName = ret[i++];
+        if (type === 'i' || type === 's') {
             rows.push({
                 type,
-                row,
-                sequenceName,
-                start: +ret[i++],
-                strand: ret[i++] === '-' ? -1 : 1,
-                sequenceLength: +ret[i++],
-            });
-        }
-        else if (type === 's') {
-            const row = +ret[i++];
-            const sequenceName = ret[i++];
-            rows.push({
-                type,
-                row,
-                sequenceName,
+                row: +ret[i++],
+                sequenceName: ret[i++],
                 start: +ret[i++],
                 strand: ret[i++] === '-' ? -1 : 1,
                 sequenceLength: +ret[i++],

package/dist/BgzipTaffyAdapter/rowInstructions.js.map

@@ -1 +1 @@
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package/dist/BigMafAdapter/BigMafAdapter.d.ts

@@ -1,5 +1,5 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { MafAdapterOptions } from '../types';
 import type { Feature, Region } from '@jbrowse/core/util';
 export default class BigMafAdapter extends BaseFeatureDataAdapter {
     setupP?: Promise<{
@@ -13,7 +13,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
     }>;
     getRefNames(): Promise<string[]>;
     getHeader(): Promise<unknown>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getFeatures(query: Region, opts?: MafAdapterOptions): import("rxjs").Observable<Feature>;
     getSamples(_query: Region): Promise<{
         samples: {
             id: string;

package/dist/BigMafAdapter/BigMafAdapter.js

@@ -1,12 +1,10 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import MafFeature from '../MafFeature';
-import parseNewick from '../parseNewick';
-import { normalize } from '../util';
 import { subscribeToObservable } from '../util/observableUtils';
 import { parseAssemblyAndChrSimple } from '../util/parseAssemblyName';
+import { getSamplesFromConfig } from '../util/getSamples';
 export default class BigMafAdapter extends BaseFeatureDataAdapter {
     setupP;
     async setup() {
@@ -28,17 +26,20 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
         return this.setupP;
     }
     async getRefNames() {
-        const { adapter } = await this.setup();
+        const { adapter } = await this.setupPre();
         return adapter.getRefNames();
     }
     async getHeader() {
-        const { adapter } = await this.setup();
+        const { adapter } = await this.setupPre();
         return adapter.getHeader();
     }
     getFeatures(query, opts) {
         const WHITESPACE_REGEX = / +/;
         return ObservableCreate(async (observer) => {
             const { adapter } = await this.setupPre();
+            const sampleFilter = opts?.samples
+                ? new Set(opts.samples.map(s => s.id))
+                : undefined;
             await subscribeToObservable(adapter.getFeatures(query, opts), feature => {
                 const maf = feature.get('mafBlock');
                 const blocks = maf.split(';');
@@ -49,10 +50,13 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
                         const parts = block.split(WHITESPACE_REGEX);
                         const sequence = parts[6];
                         const organismChr = parts[1];
+                        const { assemblyName: org, chr } = parseAssemblyAndChrSimple(organismChr);
                         if (referenceSeq === undefined) {
                             referenceSeq = sequence;
                         }
-                        const { assemblyName: org, chr } = parseAssemblyAndChrSimple(organismChr);
+                        if (sampleFilter && !sampleFilter.has(org)) {
+                            continue;
+                        }
                         alignments[org] = {
                             chr,
                             start: +parts[2],
@@ -70,16 +74,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
         }, opts?.stopToken);
     }
     async getSamples(_query) {
-        const nhLoc = this.getConf('nhLocation');
-        const nh = nhLoc.uri === '/path/to/my.nh'
-            ? undefined
-            : await openLocation(nhLoc).readFile('utf8');
-        // TODO: we may need to resolve the exact set of rows in the visible region
-        // here
-        return {
-            samples: normalize(this.getConf('samples')),
-            tree: nh ? parseNewick(nh) : undefined,
-        };
+        return getSamplesFromConfig(this.getConf.bind(this));
     }
     freeResources() { }
 }

package/dist/BigMafAdapter/BigMafAdapter.js.map

@@ -1 +1 @@
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package/dist/BigMafAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
      */
@@ -28,5 +28,5 @@ declare const configSchema: import("@jbrowse/core/esm/configuration/configuratio
             locationType: string;
         };
     };
-}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;