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Ultima develop code merge #1423

Merged
merged 27 commits into from
Dec 11, 2023
Merged

Ultima develop code merge #1423

merged 27 commits into from
Dec 11, 2023

Commits on Dec 29, 2021

  1. gradle build

    @dror27 @ilyasoifer
    dror27 authored and ilyasoifer committed Dec 29, 2021
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  2. Gradle Build in workflows

    @dror27 @ilyasoifer
    dror27 authored and ilyasoifer committed Dec 29, 2021
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  3. delete workflow put in wrong place

    @dror27 @ilyasoifer
    dror27 authored and ilyasoifer committed Dec 29, 2021
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Commits on Oct 27, 2022

  1. igv_ug_30 

    Ultima IGV Extensions

ported and refactored as extensions

WithJava added

Update gradle.yml

Update gradle.yml

Update gradle.yml

Update gradle.yml

Update gradle.yml

Update gradle.yml

Update gradle.yml

Update gradle.yml

t0 handling

guard against t0 missing

t0 processing corrected

should only apply to del of a single base and only when the deleted base is different from the two bases surrounding it. Otherwise, previous logic should be applied (now restored)

update token

M1 build added
    @dror27
    dror27 committed Oct 27, 2022
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  2. Merge branch 'master' of https://github.com/igvteam/igv into update

    @dror27
    dror27 committed Oct 27, 2022
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  3. Merge branch 'update' into ultima-develop

    @dror27
    dror27 committed Oct 27, 2022
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  4. Merge with master, when on 2.15.1 (at least)

    @dror27
    dror27 committed Oct 27, 2022
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Commits on Oct 31, 2022

  1. Fix reference access to be case independent

    @dror27
    dror27 committed Oct 31, 2022
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Commits on May 16, 2023

  1. token updated

    @dror27
    dror27 committed May 16, 2023
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Commits on Jul 21, 2023

  1. genomeId conversion to relative protection

    @dror27
    dror27 committed Jul 21, 2023
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Commits on Aug 16, 2023

  1. token update

    @dror27
    dror27 committed Aug 16, 2023
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Commits on Aug 17, 2023

  1. Remove explicit token

    @dror27
    dror27 committed Aug 17, 2023
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Commits on Oct 11, 2023

  1. java 11.0.19 update

    @dror27
    dror27 committed Oct 11, 2023
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Commits on Oct 28, 2023

  1. Merge remote-tracking branch 'igv-private/ultima-develop' into ultima… 

    …-develop
    @dror27
    dror27 committed Oct 28, 2023
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Commits on Nov 11, 2023

  1. flow renderer test/example file added. data around chr1:10000

    @dror27
    dror27 committed Nov 11, 2023
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Commits on Nov 19, 2023

  1. Documentation added

    @ilyasoifer
    ilyasoifer committed Nov 19, 2023
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Commits on Nov 20, 2023

  1. protect against "tp" tag not indicating flow

    @dror27
    dror27 committed Nov 20, 2023
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Commits on Nov 29, 2023

  1. Goto mate added

    @dror27
    dror27 committed Nov 29, 2023
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  2. show "goto mate" only for mated variants

    @dror27
    dror27 committed Nov 29, 2023
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Commits on Dec 5, 2023

  1. Revert "show "goto mate" only for mated variants" 

    This reverts commit 53e973d.
    @dror27
    dror27 committed Dec 5, 2023
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  2. Revert "Goto mate added" 

    This reverts commit d11c776.
    @dror27
    dror27 committed Dec 5, 2023
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  3. Extension framework removed

    @dror27
    dror27 committed Dec 5, 2023
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  4. Merge branch 'master' into ultima-develop

    @dror27
    dror27 committed Dec 5, 2023
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  5. add missing import

    @dror27
    dror27 committed Dec 5, 2023
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Commits on Dec 6, 2023

  1. remove LoadMultipleTracks and Relative Genome resolve ignoring

    @dror27
    dror27 committed Dec 6, 2023
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Commits on Dec 10, 2023

  1. remove drawInsertions method

    @dror27
    dror27 committed Dec 10, 2023
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  2. doc deleted from source tree

    @dror27
    dror27 committed Dec 10, 2023
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