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Viewer for sequence alignments.

Note: This is the source code for the pileup only! You might want to check out the following repositories as well:

• HiGlass viewer:https://github.com/higlass/higlass
• HiGlass server:https://github.com/higlass/higlass-server
• HiGlass docker:https://github.com/higlass/higlass-docker

npm install higlass-pileup

The live scripts can be found at:

• https://unpkg.com/higlass-pileup/dist/higlass-pileup.min.js

1. Group by strand when using single vs. paired end reads
2. Group by HP tag when using single vs. paired end reads

1. Make sure you load this track prior tohglib.js. For example:

<script src="/higlass-pileup-track.js"></script><script src="hglib.js"></script><script>  ...</script>

2. Now, configure the track in your view config and be happy!

{  "editable": true,  "trackSourceServers": [    "http://higlass.io/api/v1"  ],  "exportViewUrl": "/api/v1/viewconfs",  "views": [    {      "initialXDomain": [        0,        100000      ],      "tracks": {        "top": [          {            "type": "pileup",            "options": {              "axisPositionHorizontal": "right",              "axisLabelFormatting": "normal",              "showCoverage": false,              "colorScale": [                // A T G C N Other                "#2c7bb6",                "#92c5de",                "#ffffbf",                "#fdae61",                "#808080",                "#DCDCDC"              ]            },            "height": 180,            "uid": "FylkvVBTSumoJ959HT4-5A",            "data": {              "type": "bam",              "bamUrl": "https://pkerp.s3.amazonaws.com/public/bamfile_test/SRR1770413.sorted.bam",              "baiUrl": "https://pkerp.s3.amazonaws.com/public/bamfile_test/SRR1770413.sorted.bam.bai",              "chromSizesUrl": "https://pkerp.s3.amazonaws.com/public/bamfile_test/GCF_000005845.2_ASM584v2_genomic.chrom.sizes",              {                "options": {                  "maxTileWidth": 30000                }              }            },            "width": 470          }        ]      },      "layout": {        "w": 12,        "h": 6,        "x": 0,        "y": 0      }    }  ]}

3. To use in higlass.io:

• Modify the viewconf above to specify the URL for your BAM file.
• Either remove or update thechromSizesUrl 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).
• Save the viewconf as a JSON file.
• Navigate to higlass.io/app and drag the JSON file onto the viewer.
• Browse away!

maxTileWidth - To limit the amount of data that is fetched from the server, HiGlass sets adefault maximum tile width. This can be modified in thedata section of the track config. Settingit to a large file will let you zoom out further while still fetching data. This is useful forviewing low coverage BAM files.

colorScale - Array that controls the color of substitutions and highlighted reads. It can take 6 or 11 values. 11 values are required if you want to control highlighted read colors (see thehighlightReadsBy option). Example:

"colorScale": [  "#2c7bb6", //color of A substitutions  "#92c5de", //color of T substitutions  "#ffffbf", //color of G substitutions  "#fdae61", //color of C substitutions  "#808080", //color of N substitutions  "#DCDCDC", //color of other substitutions  "#FF0000", //color of reads with large insert size  "#0000D1", //color of reads with small insert size  "#00D1D1", //color of reads with LL orientation (see https://software.broadinstitute.org/software/igv/interpreting_pair_orientations)  "#555CFA", //color of reads with RR orientation  "#02A221", //color of reads with RL orientation]

outlineReadOnHover - Highlights the current read on hover.

outlineMateOnHover - Highlights the mate of the current read on hover. If the mate is a split read,both alignments will be highlighted.

highlightReadsBy - Array that can take the valuesinsertSize,pairOrientation orinsertSizeAndPairOrientation:

• ifinsertSize is set, reads that have a large or small insert size will be highlighted. The thresholds are controlled by thelargeInsertSizeThreshold andsmallInsertSizeThreshold track options.largeInsertSizeThreshold defaults to1000, i.e., 1000 bp.smallInsertSizeThreshold is not set by default, i.e, reads with small insert size won't be highlighted.
• ifpairOrientation is set, reads with an abnormal mapping orientation are highlighted (e.g. ++,--,-+).
• ifinsertSizeAndPairOrientation is set, reads with an abnormal mapping orientation that also have abnormal insert sizes are highlighted.
• if multiple values are set, reads that fulfill any of the conditions are highlighed in the corresponding color.
• highlight colors can be controlled by extending thecolorScale 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).

minMappingQuality - If this is set (integer), reads with a mapping quality lower than the specified value are not displayed.

Thehiglass-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 thetrack section of a viewconf:

            data: {              type: 'local-tiles',              tilesetInfo: {                'min_pos': [0],                'max_pos': [14],                'max_width': 64,                'tile_size': 1024,                'chromsizes': [['a', 14]],                'max_zoom': 0,                'max_tile_width': 100000,                'format': 'subs'              },              tiles: {                '0.0': [{                  "id": "r1",                  "from": 0,                  "to": 100,                  "substitutions": [                    {'pos': 2, 'type': 'D', 'length': 2},                    {'pos': 6, 'type': 'X', 'length': 1, 'base': 'A', 'variant': 'T'},                    {'pos': 9, 'type': 'D', 'length': 2}                  ],                  "color": 0                }],              }            }

The currently available substitution types are:

• S - corresponding to soft clipped bases
• H - corresponding to hard clipped bases
• X - corresponding to a mismatch
• I - corresponding to an insertion
• D - corresponding to a deletion

For questions, please either open an issue or ask on the HiGlass Slack channel athttp://bit.ly/higlass-slack

$ git clone https://github.com/higlass/higlass-pileup-track&& higlass-pileup-track$ npm install

Developmental server:npm startProduction build:npm run build