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You might want to check out the following repositories as well:\n\n- HiGlass viewer: https://github.com/higlass/higlass\n- HiGlass server: https://github.com/higlass/higlass-server\n- HiGlass docker: https://github.com/higlass/higlass-docker\n\n## Installation\n\n```\nnpm install higlass-pileup\n```\n\n## Usage\n\nThe live scripts can be found at:\n\n- https://unpkg.com/higlass-pileup/dist/higlass-pileup.min.js\n\n## Things that haven't been thoroughly tested\n\n1. Group by strand when using single vs. paired end reads\n2. Group by HP tag when using single vs. paired end reads\n\n### Client\n\n1. Make sure you load this track prior to `hglib.js`. For example:\n\n```\n<script src=\"/higlass-pileup-track.js\"></script>\n<script src=\"hglib.js\"></script>\n<script>\n  ...\n</script>\n```\n\n2. Now, configure the track in your view config and be happy!\n\n```\n{\n  \"editable\": true,\n  \"trackSourceServers\": [\n    \"http://higlass.io/api/v1\"\n  ],\n  \"exportViewUrl\": \"/api/v1/viewconfs\",\n  \"views\": [\n    {\n      \"initialXDomain\": [\n        0,\n        100000\n      ],\n      \"tracks\": {\n        \"top\": [\n          {\n            \"type\": \"pileup\",\n            \"options\": {\n              \"axisPositionHorizontal\": \"right\",\n              \"axisLabelFormatting\": \"normal\",\n              \"showCoverage\": false,\n              \"colorScale\": [\n                // A T G C N Other\n                \"#2c7bb6\",\n                \"#92c5de\",\n                \"#ffffbf\",\n                \"#fdae61\",\n                \"#808080\",\n                \"#DCDCDC\"\n              ]\n            },\n            \"height\": 180,\n            \"uid\": \"FylkvVBTSumoJ959HT4-5A\",\n            \"data\": {\n              \"type\": \"bam\",\n              \"bamUrl\": \"https://pkerp.s3.amazonaws.com/public/bamfile_test/SRR1770413.sorted.bam\",\n              \"baiUrl\": \"https://pkerp.s3.amazonaws.com/public/bamfile_test/SRR1770413.sorted.bam.bai\",\n              \"chromSizesUrl\": \"https://pkerp.s3.amazonaws.com/public/bamfile_test/GCF_000005845.2_ASM584v2_genomic.chrom.sizes\",\n              {\n                \"options\": {\n                  \"maxTileWidth\": 30000\n                }\n              }\n            },\n            \"width\": 470\n          }\n        ]\n      },\n      \"layout\": {\n        \"w\": 12,\n        \"h\": 6,\n        \"x\": 0,\n        \"y\": 0\n      }\n    }\n  ]\n}\n```\n\n3. To use in higlass.io:\n\n- Modify the viewconf above to specify the URL for your BAM file.\n- Either remove or update the `chromSizesUrl` entry to point to a chromosome sizes file for the assembly that your BAM file is aligned to. If it's omitted, the chromosome sizes will be extracted directly from the BAM file and ordered best-guess semantically (i.e. chr1, chr2, ...., chrM, chrX, chrY).\n- Save the viewconf as a JSON file.\n- Navigate to higlass.io/app and drag the JSON file onto the viewer.\n- Browse away!\n\n## Options\n\n### Data config\n\n**maxTileWidth** - To limit the amount of data that is fetched from the server, HiGlass sets a\ndefault maximum tile width. This can be modified in the `data` section of the track config. Setting\nit to a large file will let you zoom out further while still fetching data. This is useful for\nviewing low coverage BAM files.\n\n### Track options\n\n**colorScale** - Array that controls the color of substitutions and highlighted reads. It can take 6, 11, 21, or 26 values:\n- 6 values: DNA bases (A, T, G, C, N, other)\n- 11 values: DNA bases + highlighted read colors (see `highlightReadsBy` option)\n- 21 values: Protein amino acids (ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, STOP)\n- 26 values: Protein amino acids + highlighted read colors\n\nDNA example:\n```\n\"colorScale\": [\n  \"#2c7bb6\", //color of A substitutions\n  \"#92c5de\", //color of T substitutions\n  \"#ffffbf\", //color of G substitutions\n  \"#fdae61\", //color of C substitutions\n  \"#808080\", //color of N substitutions\n  \"#DCDCDC\", //color of other substitutions\n  \"#FF0000\", //color of reads with large insert size\n  \"#0000D1\", //color of reads with small insert size\n  \"#00D1D1\", //color of reads with LL orientation\n  \"#555CFA\", //color of reads with RR orientation\n  \"#02A221\", //color of reads with RL orientation\n]\n```\n\nProtein example:\n```\n\"colorScale\": [\n  \"#CCCCCC\", //ALA - Alanine\n  \"#0000FF\", //ARG - Arginine (basic)\n  \"#00FFFF\", //ASN - Asparagine (polar)\n  \"#FF0000\", //ASP - Aspartic acid (acidic)\n  \"#FFFF00\", //CYS - Cysteine (sulfur)\n  \"#00FFFF\", //GLN - Glutamine (polar)\n  \"#FF0000\", //GLU - Glutamic acid (acidic)\n  \"#E6E6E6\", //GLY - Glycine (small)\n  \"#0000FF\", //HIS - Histidine (basic)\n  \"#00FF00\", //ILE - Isoleucine (hydrophobic)\n  \"#00FF00\", //LEU - Leucine (hydrophobic)\n  \"#0000FF\", //LYS - Lysine (basic)\n  \"#00FF00\", //MET - Methionine (hydrophobic)\n  \"#00FF00\", //PHE - Phenylalanine (hydrophobic)\n  \"#FF8000\", //PRO - Proline (special)\n  \"#00FFFF\", //SER - Serine (polar)\n  \"#00FFFF\", //THR - Threonine (polar)\n  \"#00FF00\", //TRP - Tryptophan (hydrophobic)\n  \"#00FFFF\", //TYR - Tyrosine (polar)\n  \"#00FF00\", //VAL - Valine (hydrophobic)\n  \"#000000\"  //STOP - Stop codon\n]\n```\n\n**outlineReadOnHover** - Highlights the current read on hover.\n\n**outlineMateOnHover** - Highlights the mate of the current read on hover. If the mate is a split read,\nboth alignments will be highlighted.\n\n**highlightReadsBy** - Array that can take the values `insertSize`, `pairOrientation` or `insertSizeAndPairOrientation`:\n\n- if `insertSize` is set, reads that have a large or small insert size will be highlighted. The thresholds are controlled by the `largeInsertSizeThreshold` and `smallInsertSizeThreshold` track options. `largeInsertSizeThreshold` defaults to `1000`, i.e., 1000 bp. `smallInsertSizeThreshold` is not set by default, i.e, reads with small insert size won't be highlighted.\n- if `pairOrientation` is set, reads with an abnormal mapping orientation are highlighted (e.g. ++,--,-+).\n- if `insertSizeAndPairOrientation` is set, reads with an abnormal mapping orientation that also have abnormal insert sizes are highlighted.\n- if multiple values are set, reads that fulfill any of the conditions are highlighed in the corresponding color.\n- highlight colors can be controlled by extending the `colorScale` track option to 11 values. The additional 5 values will control the large insert size color, small insert size color and the ++, --, -+ mapping orientations (in that order).\n\n**minMappingQuality** - If this is set (integer), reads with a mapping quality lower than the specified value are not displayed.\n\n### Read labels\n\nRead labels display per-read text annotations directly on the pileup track. Labels are rendered with intelligent collision detection so that only non-overlapping labels are shown; when space is limited, labels with higher importance (determined by a stable hash of the read ID) are kept visible.\n\n**readLabels** - Controls which fields are shown in the label. Set to an object with `fields` and `separator` keys to enable labels, or `null` to disable (default).\n\nAvailable fields: `id`, `pos`, `strand`, `mapq`, `readName`, or any custom field present on the read object.\n\n```json\n\"readLabels\": {\n  \"fields\": [\"readName\", \"mapq\"],\n  \"separator\": \" | \"\n}\n```\n\n**readLabelPosition** - Where the label text is anchored relative to the read body. One of `\"left\"`, `\"center\"` (default), or `\"right\"`.\n\n- `\"left\"` — label starts at the left edge of the read\n- `\"center\"` — label is centred over the read (default)\n- `\"right\"` — label ends at the right edge of the read\n\n**maxReadLabels** - Maximum number of labels shown at once (default: `200`). Lowering this improves performance in dense regions.\n\n**readLabelFontSize** - Font size in pixels (default: `10`).\n\n**readLabelFontFamily** - Font family (default: `\"Arial\"`).\n\n**readLabelColor** - Label text color as a hex integer (default: `0x333333`).\n\n**readLabelStrokeColor** - Color of the text outline, which improves legibility over reads (default: `0xffffff`).\n\n**readLabelStrokeThickness** - Thickness of the text outline in pixels (default: `2`).\n\nFull example with all label options:\n\n```json\n\"options\": {\n  \"readLabels\": {\n    \"fields\": [\"readName\", \"pos\", \"strand\", \"mapq\"],\n    \"separator\": \" \"\n  },\n  \"readLabelPosition\": \"left\",\n  \"maxReadLabels\": 100,\n  \"readLabelFontSize\": 10,\n  \"readLabelFontFamily\": \"Arial\",\n  \"readLabelColor\": 3355443,\n  \"readLabelStrokeColor\": 16777215,\n  \"readLabelStrokeThickness\": 2\n}\n```\n\n## Click Handler API\n\nThe pileup track automatically publishes click events with detailed read information. You can subscribe to these events to implement custom click interactions.\n\n### Subscribing to Click Events (Recommended)\n\nThe easiest way to handle clicks is to subscribe to the `app.trackClick` event published by the track:\n\n```javascript\n// Get the HiGlass viewer and track reference\nconst hgv = hglib.viewer(element, viewConfig);\n\n// Wait for track to initialize, then subscribe to click events\nsetTimeout(() => {\n  const track = hgv.getTrackObject(viewId, trackId);\n  \n  if (track && track.pubSub) {\n    track.pubSub.subscribe('app.trackClick', (eventData) => {\n      console.log('Genomic position:', eventData.data.genomicPosition);\n      console.log('Chromosome position:', eventData.data.chrPosition);\n      \n      if (eventData.data.read) {\n        console.log('Read ID:', eventData.data.read.id);\n        console.log('Position:', eventData.data.read.from, '->', eventData.data.read.to);\n        console.log('MAPQ:', eventData.data.read.mapq);\n        console.log('Strand:', eventData.data.read.strand);\n        \n        // Access substitutions\n        if (eventData.data.substitution) {\n          console.log('Substitution type:', eventData.data.substitution.type);\n          console.log('Substitution position:', eventData.data.substitution.pos);\n        }\n        \n        // Access extra BAM fields\n        if (eventData.data.read.extra) {\n          console.log('Extra fields:', eventData.data.read.extra);\n        }\n      }\n    });\n  }\n}, 1000);\n```\n\n### Event Data Structure\n\nThe `app.trackClick` event provides an object with the following structure:\n\n```javascript\n{\n  trackId: 'track-id',        // Track identifier\n  trackUid: 'track-id',       // Track unique identifier\n  viewId: 'view-id',          // View identifier\n  viewUid: 'view-id',         // View unique identifier\n  data: {\n    genomicPosition: 123456,  // Genomic coordinate (number)\n    chrPosition: ['chr1', 123456],  // [chromosome name, position]\n    read: {                   // Full read object (null if no read at click position)\n      id: 'read-id',\n      from: 123000,\n      to: 123500,\n      mapq: 60,\n      strand: '+',\n      row: 5,\n      groupKey: 'group-key',\n      chrName: 'chr1',        // If available\n      chrOffset: 0,           // If available\n      substitutions: [...],   // Array of all substitutions in read\n      mate_ids: [...],        // Mate read IDs for paired-end reads\n      extra: {...}            // Additional BAM tags\n    },\n    substitution: {           // Nearest substitution within 10px (null if none)\n      type: 'X',              // 'X'=mismatch, 'D'=deletion, 'I'=insertion, 'S'=soft clip, 'H'=hard clip\n      pos: 45,                // Position relative to read start\n      length: 1,\n      base: 'A',              // Reference base (for mismatches)\n      variant: 'T'            // Variant base (for mismatches)\n    }\n  }\n}\n```\n\n### Using getMouse Directly (Advanced)\n\nYou can also call the `getMouse` method directly for more control:\n\n```javascript\n// Get a reference to the track\nconst track = hgv.getTrackObject(viewId, trackId);\n\n// Call getMouse with track coordinates\ntrack.getMouse(trackX, trackY, (result) => {\n  console.log('Genomic position:', result.genomicPosition);\n  if (result.read) {\n    console.log('Read ID:', result.read.id);\n    // ... process read and substitution data\n  }\n});\n```\n\n### Method Signature\n\n```javascript\ngetMouse(trackX, trackY, callback)\n```\n\n**Parameters:**\n- `trackX` (number): X coordinate in track space\n- `trackY` (number): Y coordinate in track space  \n- `callback` (function, optional): Callback function that receives the result object with read data\n\n**Returns:** An object with genomic and chromosome position (synchronous). If a callback is provided, it will be called with the complete result including read and substitution data.\n\n### Return Value\n\nThe `getMouse` method returns an object immediately with position data, and optionally calls the callback with the full result:\n\n- **`genomicPosition`** (number): The genomic coordinate at the click position\n- **`chrPosition`** (array): The chromosome position as `[chromosomeName, position]`\n- **`read`** (object | null): Full read information if a read is under the cursor, or `null` if none\n- **`substitution`** (object | null): Substitution information if one is under the cursor (within 10px), or `null` if none\n\nNote: Since read data may need to be fetched asynchronously from a worker thread, the callback pattern ensures you always receive the complete data. If the data is cached (e.g., from a recent hover), the callback is called immediately.\n\n### Example\n\n```javascript\n// Using callback pattern (recommended)\ntrack.getMouse(trackX, trackY, (result) => {\n  console.log('Genomic position:', result.genomicPosition);\n  console.log('Chromosome position:', result.chrPosition);\n  \n  if (result.read) {\n    console.log('Read ID:', result.read.id);\n    console.log('Read position:', result.read.from, '-', result.read.to);\n    console.log('MAPQ:', result.read.mapq);\n    console.log('Strand:', result.read.strand);\n    \n    if (result.substitution) {\n      console.log('Nearest substitution type:', result.substitution.type);\n      console.log('Substitution position:', result.substitution.pos);\n      if (result.substitution.variant) {\n        console.log('Base change:', result.substitution.base, '->', result.substitution.variant);\n      }\n    }\n  }\n});\n\n// Immediate return value (position only, read data populated asynchronously)\nconst immediate = track.getMouse(trackX, trackY);\nconsole.log('Position:', immediate.genomicPosition); // Available immediately\nconsole.log('Read:', immediate.read); // May be null until async fetch completes\n```\n\n### Read Object Properties\n\nWhen a read is present, the read object contains:\n\n- `id`: Read identifier\n- `from`: Start genomic position\n- `to`: End genomic position\n- `mapq`: Mapping quality score\n- `strand`: Read strand ('+' or '-')\n- `row`: Visual row the read is displayed on\n- `groupKey`: Group identifier\n- `chrName`: Chromosome name (if available)\n- `chrOffset`: Chromosome offset (if available)\n- `substitutions`: Array of substitution objects\n- `mate_ids`: Array of mate read IDs (for paired-end reads)\n- `extra`: Additional BAM tags and fields\n\n### Substitution Object Properties\n\nWhen a substitution is present, the substitution object contains:\n\n- `pos`: Position relative to read start\n- `type`: Substitution type ('X' for mismatch, 'D' for deletion, 'I' for insertion, 'S' for soft clip, 'H' for hard clip)\n- `length`: Length of the substitution\n- `base`: Reference base (for mismatches)\n- `variant`: Variant base (for mismatches)\n\n## Local tiles\n\nThe `higlass-pileup` track supports local tiles. Local tiles can contain either BAM formatted data or they can include raw rendering objects. The following is a snippet that goes in the `track` section of a viewconf:\n\n```\n            data: {\n              type: 'local-tiles',\n              tilesetInfo: {\n                'min_pos': [0],\n                'max_pos': [14],\n                'max_width': 64,\n                'tile_size': 1024,\n                'chromsizes': [['a', 14]],\n                'max_zoom': 0,\n                'max_tile_width': 100000,\n                'format': 'subs'\n              },\n              tiles: {\n                '0.0': [{\n                  \"id\": \"r1\",\n                  \"from\": 0,\n                  \"to\": 100,\n                  \"substitutions\": [\n                    {'pos': 2, 'type': 'D', 'length': 2},\n                    {'pos': 6, 'type': 'X', 'length': 1, 'base': 'A', 'variant': 'T'},\n                    {'pos': 9, 'type': 'D', 'length': 2}\n                  ],\n                  \"color\": 0\n                }],\n              }\n            }\n```\n\nThe currently available substitution types are:\n\n- `S` - corresponding to soft clipped bases\n- `H` - corresponding to hard clipped bases\n- `X` - corresponding to a mismatch\n- `I` - corresponding to an insertion\n- `D` - corresponding to a deletion\n\n## HTTP tiles\n\nThe `higlass-pileup` track supports pre-rendered tiles served over HTTP. This allows tiles to be pre-computed and hosted as static files (e.g. on S3), avoiding the need for a running HiGlass server.\n\n```\ndata: {\n  type: 'http-tiles',\n  tilesetInfo: 'https://example.com/tiles/tileset_info.json',\n  tiles: {\n    '0.0': 'https://example.com/tiles/tile_0_0.json',\n    '1.0': 'https://example.com/tiles/tile_1_0.json',\n    '1.1': 'https://example.com/tiles/tile_1_1.json'\n  }\n}\n```\n\n- **`tilesetInfo`** - URL to a JSON file describing the tileset. The standard HiGlass tileset info fields are supported (`max_width`, `tile_size`, `max_zoom`, `chromsizes`, etc.). If the server returns `max_pos` instead of `max_width`, it will be normalized automatically.\n- **`tiles`** - Object mapping tile IDs (e.g. `\"0.0\"`, `\"1.3\"`) to URLs. Each URL should point to a JSON file containing an array of read objects in the same format used by [local tiles](#local-tiles).\n\nBoth `tilesetInfo` and tile URLs support gzip-compressed JSON (files ending in `.gz`).\n\nThe tile data format is the same as for local tiles — an array of read objects:\n\n```json\n[\n  {\n    \"id\": \"read1\",\n    \"from\": 1000,\n    \"to\": 1150,\n    \"row\": 0,\n    \"substitutions\": [\n      { \"pos\": 10, \"type\": \"X\", \"length\": 1, \"base\": \"A\", \"variant\": \"T\" },\n      { \"pos\": 40, \"type\": \"D\", \"length\": 3 }\n    ],\n    \"color\": 0\n  }\n]\n```\n\nIncluding a `row` field in each read allows the track to skip row assignment on the main thread, which significantly improves rendering performance for large datasets.\n\n## Protein Support\n\nThe pileup track now supports protein sequences with a 21-color amino acid color scale. The colors are mapped to amino acids based on their chemical properties:\n\n- **Basic amino acids** (ARG, HIS, LYS): Blue\n- **Acidic amino acids** (ASP, GLU): Red  \n- **Polar amino acids** (ASN, GLN, SER, THR, TYR): Cyan\n- **Hydrophobic amino acids** (ILE, LEU, MET, PHE, TRP, VAL): Green\n- **Special amino acids** (CYS, PRO): Yellow/Orange\n- **Small amino acids** (ALA, GLY): Gray\n- **Stop codons**: Black\n\n## Support\n\nFor questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack\n\n## Development\n\n### Installation\n\n```bash\n$ git clone https://github.com/higlass/higlass-pileup-track && higlass-pileup-track\n$ npm install\n```\n\n### Commands\n\n**Developmental server**: `npm start`\n**Production build**: `npm run build`\n","readmeFilename":"README.md"}