New Features
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Extended support for bedpe and UCSC interact and bigInteract formats
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Add "Sort by gap size" option to alignment track context (right-click) menu.
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New browser API method to fetch the current genomic region(s) in view.
browser.currerntLoci() -
Support CSI index for BAM files.
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Show GFF "gene" features if not part of a composite feature or features (such as trasnscript).
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Enable normalization of coverage tracks (#1153).
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API to sort alignment tracks by base (#893).
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Option to load specific samples for segmented copy number tracks (#814).
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Property values in track configuration objects now have precedence over property values from "track line". (#994, #1068).
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Support UCSC
useScoreoption (#869). -
Add "squished view" option for BAM tracks (#160).
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Support setting color (
altColor) for negative strand features (#1149)