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Add new coloring options for dotplot and ability to "rectangularize" dotplot view #2791

Merged
merged 26 commits into from
Mar 9, 2022
Merged

Add new coloring options for dotplot and ability to "rectangularize" dotplot view #2791

merged 26 commits into from
Mar 9, 2022

Commits on Mar 9, 2022

  1. Dotplot mods

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  2. Updates

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  3. Draw open circles for large CIGAR

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  4. Remove ctrl+scroll in dotplot

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  5. Misc

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  6. Add method to only connect indels of a certain size

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  7. Add a br breakpoint in dotplot header

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  8. Large indel limit

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  9. More misc

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  10. Ticks

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  11. Add dotplot renderer line width

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  12. Fix lint

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  13. Put target assembly on x-axis for dotplot

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  14. Color by qual

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  15. Line width 2.5

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  16. Re-organize paf record

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  17. Update comment

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  18. Thresholds config editing

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  19. Less circles

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  20. Create MashMap adapter, since mashmap doesn't follow the format of paf 

    after col 9, this let's us load score more reliably
    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  21. Remove large indel limit

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  22. Back to main

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  23. Code simplify

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  24. Add ability to load MCScan .anchors and .anchors.simple files using t… 

    …he GUI import forms for dotplot/synteny views (#2792)


* Update mcscan anchors adapter to take a bed1Location and bed2Location

* Standardize on left and right columns for mcscan anchors

* Improve anchors importing

* Add simple anchors example

* Add simple anchors to import form

* Update mcscan synteny config

* Add delta example to grape vs peach dotplot
    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  25. T1

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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  26. Unify simpleanchors and anchors somewhat

    @cmdcolin
    cmdcolin committed Mar 9, 2022
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