Interact feature refactor - #1720
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Pull Request Overview
This PR refactors and consolidates support for inter-chromosomal interaction (BEDPE) data by introducing a generic BedPE interface, new parsers/codecs, and integrating Interact/BEDPE features into BigBed files and the rendering pipeline.
- Introduce BedPE, BedPEFeature, InteractFeature, InteractParser, InteractCodec, and BedPESource for generic interaction feature support.
- Update BBFile, BBCodecFactory, and add BBInteractCodec to handle “interact” bigBed formats.
- Modify TrackLoader, FeatureSource, and InteractionTrack to load, cache, and render interaction tracks.
Reviewed Changes
Copilot reviewed 57 out of 57 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| src/main/java/org/broad/igv/bedpe/BedPESource.java | New FeatureSource implementation for generic BedPE data |
| src/main/java/org/broad/igv/bedpe/InteractParser.java | New parser for UCSC interact text files |
| src/main/java/org/broad/igv/track/TrackLoader.java | Updated to recognize “interact” format and use BedPESource |
Comments suppressed due to low confidence (2)
src/main/java/org/broad/igv/bedpe/BedPESource.java:1
- [nitpick] BedPESource is a new core class but lacks dedicated unit tests; consider adding tests to validate feature retrieval and downsampling.
package org.broad.igv.bedpe;
src/main/java/org/broad/igv/bedpe/InteractCodec.java:55
- [nitpick] canDecode always returns true, which may cause this codec to attempt decoding unsupported files; refine it to check file extension or header pattern.
return true;
| } else if (format.equals("bw") || format.equals("bb") || format.equals("bigwig") || | ||
| format.equals("bigbed") || format.equals("biggenepred") || format.equals("bigrepmsk")) { | ||
| loadBWFile(locator, newTracks, genome); | ||
| loadBBFile(locator, newTracks, genome); |
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[nitpick] The method loadBBFile now handles both BigWig and BigBed formats but the name 'loadBBFile' is misleading; consider renaming to reflect its dual role or splitting into separate methods.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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