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Commits on Oct 24, 2019

• Protect against IGV startup failure when IGV google oauth properties can't be loaded. This can happen when IGV cannot open a network connection.

  jrobinso

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Commits on Oct 22, 2019

• update url mappings to eliminate cloudfront -- too flaky

  jrobinso

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• update b37 genome path

  jrobinso

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Commits on Oct 21, 2019

• Fix line plot error (see igvteam#715)

  jrobinso

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• Increase scroll increment in preferences window. (igvteam#716)

  

  Lenbok

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  jrobinso

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Commits on Oct 16, 2019

• remove unused code

  jrobinso

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Commits on Oct 12, 2019

• Faster s3 load dialog (igvteam#711)

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  brainstorm

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  jrobinso

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Commits on Oct 11, 2019

• update htsjdk jar (breaking change)

  jrobinso

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• Update VCF popup text to recognize htsjdk value for "missing". Fixes igvteam#628

  jrobinso

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• correctly place gene names in multi-locus batch snapshots. Fixes igvteam#633

  jrobinso

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• genome and load-from-server updates

  jrobinso

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• Fix bugs with genome selection from a batch script. (1) selection ignored if the genome ID was not already in the selection list, (2) url paths to genomes or fastas didn't work with "genome" command.

  jrobinso

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• Bug fix -- certain preferences set from a batch script were ignored for 3rd gen and RNA alignment tracks. Fixes igvteam#640.

  jrobinso

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Commits on Oct 10, 2019

• AWS glacier UX fix (igvteam#710)

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  brainstorm

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  jrobinso

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Commits on Oct 8, 2019

• catch error when removing provisioning URL (don't try to load "")

  jrobinso

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• Oauth refactor (igvteam#708)

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  jrobinso

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• * Save showDataRange in session

  jrobinso

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• Fix group autoscale bug for overlaid tracks from a session. Fixes igvteam#694

  jrobinso

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Commits on Oct 6, 2019

• remove deprecated "SEARCH_ZOOM" option. Fixes igvteam#684

  jrobinso

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• increase pref edit width to see all tabs

  jrobinso

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• line plot issue -- fixes igvteam#682

  jrobinso

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Commits on Oct 5, 2019

• bug inferring cram index

  jrobinso

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Commits on Oct 4, 2019

• Cleanup imputation of bam file index urls

  jrobinso

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Commits on Oct 3, 2019

• NSIS update to install shortcuts etc for all users (igvteam#707)

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  davideby

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  jrobinso

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• Use chromosome aliasing for regions-of-interest. Fixes igvteam#700

  jrobinso

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• Fix for issue igvteam#704 -- tabix index guessing for s3 files

  jrobinso

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• fix some index path logic

  jrobinso

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• minor cleanup of OAuthUtils, remove dead code

  jrobinso

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• support public google urls (don't pre-emptively force login)

  jrobinso

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• remove debug statements

  jrobinso

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• move urlhelper setting to "Main" class -- earlier in startup process

  jrobinso

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• debug statements

  jrobinso

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• patch the htsjdk -- current release is broken for java 11. Add alternative to using reflection for URLHelper, forbidden across modules in Java 11.

  jrobinso

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• Revert "Cleanup the exclusion, version bump htsjdk from mavencentral and kill the last (htsjdk) jar remaining under lib/ (igvteam#692)"

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  jrobinso

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Commits on Oct 2, 2019

• more logging

  jrobinso

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