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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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color alignments by secondary/supplementary alignment orientation #775

Open jrobinso opened 4 years ago

jrobinso commented 4 years ago

Split off from #632. Some copied comments follow

@oneillkza says...

color alignments by secondary/supplementary alignment orientation" The "color alignments by mate orientation" feature is also really useful; it would be great to have something similar for split long reads

@amwenger says...

One way to accomplish this would be to use different colors for the ends of clipped alignments (currently always magenta) based on how the clipped portion of the read aligns: rest of the read does not align rest of the read aligns downstream in the reference on the same strand without skipping read sequence (DELETION) rest of the read aligns upstream in the reference on the same strand without skipping read sequence (DUPLICATION) rest of the read aligns nearby in the reference on the same strand and skips read sequence (INSERTION) rest of the read aligns nearby in the reference on the opposite strand without skipping read sequence (INVERSION) rest of the read aligns far away in the reference (TRANSLOCATION)

oneillkza commented 4 years ago

Thanks @jrobinso . Also, @amwenger has done a great job of capturing the kind of information that's needed to be represented.

olechnwin commented 3 years ago

Sorry I have to ask. I'm guessing this feature has not been implemented yet? I just downloaded version 2.9.4 and there is no option to color by supplementary alignment. Thank you!

jrobinso commented 3 years ago

@olechnwin No it hasn't. When it has this will be closed.