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Commits on Jan 11, 2022

• Merge branch 'igvteam:master' into master

  lindenb

  authored
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Commits on Jan 3, 2022

• enable port listener if circ view is enabled

  jrobinso

  committed
  4e6839e

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• Determine track type by actual track instance type, rather than its data file path

  jrobinso

  committed
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Commits on Dec 31, 2021

• Logging cleanup -- distinguish warnning and info messages.

  jrobinso

  committed
  de0c59a

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• Add support for leading tilda (~) in session genome and resource (track) paths. ~ will be replaced by System.getProperty("user.home"). Fixes igvteam#1056

  jrobinso

  committed
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Commits on Dec 30, 2021

• Rearrange alignment menu copy & blat items

  jrobinso

  committed
  3535e7e

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• * Apply wait cursor for long running batch and port commands

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  jrobinso

  committed
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Commits on Dec 29, 2021

• Implement downsampling for the whole genome view for interaction (bedpe) tracks. This prevents IGV crash when tying to draw large numbers of arcs which can't be distinguished in any event. Also imp…

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  jrobinso

  committed
  c7724de

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Commits on Dec 28, 2021

• Fix spurious drag&drop error messages

  jrobinso

  committed
  c21b784

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Commits on Dec 27, 2021

• Remove unused test data

  jrobinso

  committed
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Commits on Dec 24, 2021

• ignore all htsget unit tests -- there are either problems with the reference server or network

  jrobinso

  committed
  4da4501

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• htsget reader unit test problem

  jrobinso

  committed
  f4717c7

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• * Circview updates -- better support for BedPE (interaction / arc tracks)

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  jrobinso

  committed
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Commits on Dec 22, 2021

• proguard typo

  jrobinso

  committed
  6dbf686

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Commits on Dec 21, 2021

• Remove some unused dependencies

  jrobinso

  committed
  04a2b5b

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• .

  jrobinso

  committed
  8110d56

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• Remove unsupported "Goby" files

  jrobinso

  committed
  e0a7873

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• Excluding Log4J from dependencies packaged into the bundles

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  davideby

  committed
  2494af5

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• Exclude all Log4J jars from the bundles

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  davideby

  committed
  19e3bfe

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Commits on Dec 20, 2021

• temp removal of circview contents

  jrobinso

  committed
  8bf2a9a

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• logging comments and cleanup

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  jrobinso

  committed
  22afd12

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• Restore sample size for alignment track type determination to 1,000, this cost nothing.

  jrobinso

  committed
  cf2050f

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• circ view -- combine overlapping loci from interactions between nearby loci

  jrobinso

  committed
  f492721

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• Remove log4j -- 3 high level vulnerabilities in 6 days.

  jrobinso

  committed
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• BAN reading optimizations

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  jrobinso

  committed
  51a901e

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• Make chord click -> frames additive

  jrobinso

  committed
  fe2de0c

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• circ view user preferences

  jrobinso

  committed
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Commits on Dec 15, 2021

• prefs update

  jrobinso

  committed
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• Disable "color by insert size" for RNA alignment tracks -- insert size is not intrepretable for RNA as pairs can span exons

  jrobinso

  committed
  84a29e9

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• Close port listener on oAuth flow completion if port enabled = false

  jrobinso

  committed
  a8ba755

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• simplify CommandListener

  jrobinso

  committed
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• Enable port listener if oAuth page is opened, as its required for oAuth flow to work.

  jrobinso

  committed
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Commits on Dec 14, 2021

• Updated to Log4J 2.16.0 libraries

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  davideby

  committed
  ea89b06

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• Apply port listener preference changes immediately

  jrobinso

  committed
  497ea62

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Commits on Dec 13, 2021

• disable port listener by default

  jrobinso

  committed
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