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Commits on Sep 20, 2024

• Update CRAM reference test to include a genbank (gbk) referece with chromosome aliasing

  jrobinso

  committed
  4448888

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Commits on Sep 16, 2024

• Replace compiled shell script MacOS launcher

  jrobinso

  authored
  068e20a

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Commits on Sep 15, 2024

• Update mac startup script for jdk 21

  jrobinso

  committed
  e16fd78

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Commits on Sep 14, 2024

• Update jdk-17 references to jdk-21

  jrobinso

  committed
  bfd072f

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Commits on Sep 13, 2024

• remove test generated file

  jrobinso

  committed
  b3689ee

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• Update to Java 21 and gradle 8.10.1 (#1568)

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  lbergelson

  authored
  e658784

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Commits on Sep 10, 2024

• Genome loading refactor to recover gracefully on startup errors (#1553)

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  jrobinso

  authored
  e8e38e1

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• Add basemod colors for 3 chebi codes. See #1563 (#1566)

  jrobinso

  authored
  5a9c3ec

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• Improve behavior of the Hide small indels menu option (#1564)

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  lbergelson

  authored
  97dd56d

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• disable snappy 3

  jrobinso

  committed
  5b18361

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Commits on Sep 9, 2024

• disable snappy, second attempt

  jrobinso

  committed
  4521c92

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• Disable "snappy" for command line igvtools

  jrobinso

  committed
  c265c9d

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• Remove "snappy" dependency

  jrobinso

  committed
  ab89ab9

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Commits on Sep 8, 2024

• Refactor BB reader to conform more closely to spec -- no assumptions on the layout of the file, particularly the relative location of the chromosome B+ tree.

  jrobinso

  committed
  1bb1bd1

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• Changes to support BB files with alternative layouts, specifically chromTree following the full data section.

  jrobinso

  committed
  8b364e7

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Commits on Sep 5, 2024

• Delete unused Apache Tomcat Utils package (#1562)

  lbergelson

  authored
  1767b02

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Commits on Sep 4, 2024

• Look for "TS" attribute to determine transcript strand. See #1558

  jrobinso

  committed
  15d7569

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• Introduce hidden preference for default oAuth provisioning url

  jrobinso

  committed
  7aca9ea

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Commits on Sep 1, 2024

• Display unrecognized modifications in popup text

  jrobinso

  committed
  c597d32

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Commits on Aug 20, 2024

• Simplify genome selection dialog

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  jrobinso

  committed
  916c173

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• Unit test maintenance

  jrobinso

  committed
  4a739bf

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• Alignment track - don't repack on drag unless in FULL mode

  jrobinso

  committed
  3f4d87b

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Commits on Aug 18, 2024

• SpliceJunction tracks now honor manual color setttings (#1546)

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  lbergelson

  authored
  0d4375d

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• Adding additional options for duplicate reads. (#1542)

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  lbergelson

  authored
  cc37d33

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Commits on Aug 16, 2024

• Use specifed nameSet, if specified, for whole genome and pulldown chromosome names.

  jrobinso

  committed
  1ed0fc4

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Commits on Aug 15, 2024

• Update dependencies to fix vulnerabilities (#1544)

  lbergelson

  authored
  b611dbc

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Commits on Aug 14, 2024

• Move the amazon credentials check at startup into an async thread (#1543)

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  lbergelson

  and

  jrobinso

  authored
  d372765

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• Clarify zoom in instructions for whole genome view. Fixes #1539

  jrobinso

  committed
  b730c8a

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• Fix logic searching for features containing a position. Fixes #1541

  jrobinso

  committed
  71e111a

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Commits on Aug 13, 2024

• Fix unit tests and issue with "chrom.sizes" genomes.

  jrobinso

  committed
  1a426ee

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Commits on Aug 12, 2024

• compute long chr names for chrom.sizes file

  jrobinso

  committed
  8c599b8

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• Clip splice junction arcs at junction boundaries. Fix for Bezier curve artifact that sometimes carries curve behond junction boundaries. Fixes #1535

  jrobinso

  committed
  7663069

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Commits on Aug 3, 2024

• Restore center-on-click to ruler panel. Fixes #1538

  jrobinso

  committed
  fa87234

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Commits on Jul 30, 2024

• Cleanup git ignore

  jrobinso

  committed
  bf7f46f

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Commits on Jul 26, 2024

• Proxy server for testing.

  jrobinso

  committed
  b1510d0

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