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jrobinso

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Commits on Apr 13, 2024

• ditto

  jrobinso

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  491e201

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Commits on Apr 12, 2024

• Use invokeLater to hide / show glass pane (i.e. wait cursor pane). Fixes bug reported on igv-help

  jrobinso

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  d9bea5b

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Commits on Apr 10, 2024

• Bug fix -- maximum coverage estimate effecting whole genome view for sparsely populated feature files.

  jrobinso

  committed
  a5cf045

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Commits on Apr 4, 2024

• Bug fix - improper chromosome version aliasing

  jrobinso

  committed
  48491bb

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Commits on Mar 24, 2024

• Add base modification options to alignment track preferences (defaults)

  jrobinso

  committed
  b0c9acf

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Commits on Mar 20, 2024

• Bigwig performance fix -- see issue igvteam#1505

  jrobinso

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  6015ca7

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Commits on Mar 19, 2024

• Add bigwig stress test session

  jrobinso

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  379f8a1

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Commits on Mar 7, 2024

• TDF null check

  jrobinso

  committed
  3fe375f

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• .

  jrobinso

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  8ee6ecd

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• bug fix -- ChromAliasManager could return "null" for an alias, not expected by callers.

  jrobinso

  committed
  6f7cb50

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Commits on Mar 5, 2024

• Genome menu changes (GenArk)

  jrobinso

  committed
  32f93de

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• Support chromosome pulldown for GenArk assemblies

  jrobinso

  committed
  a716f73

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• Fix bug caused by calculating genomic range of a reference frame prior to frame having a width in pixels.

  jrobinso

  committed
  55d25f3

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Commits on Mar 1, 2024

• Searchable table - correct tooltip text, code cleanup

  jrobinso

  committed
  5460677

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• typo

  jrobinso

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  d827f74

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• Rename GenArk menu item

  jrobinso

  committed
  cf8469f

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• Create "psuedo" cytoband to enable ideogram navigation for assemblies with no cytoband file. Maintains pre 2.17 compatibility. Fixes igvteam#1498

  jrobinso

  committed
  18616bf

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• Fix logic validating MM tags on negative strand alignments. See igvteam#1476

  jrobinso

  committed
  455dc00

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Commits on Feb 26, 2024

• Sashimi plot layout changes.

  jrobinso

  committed
  f77a27f

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Commits on Feb 22, 2024

• Fix performance issue with sashimi plot SVG output.

  jrobinso

  committed
  2feb7e2

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Commits on Feb 20, 2024

• Add UCSC GenArk search widget

  jrobinso

  committed
  ff5f7f4

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Commits on Feb 8, 2024

• Array index check. See igvteam#1488

  jrobinso

  committed
  cb33d05

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• Fix broken unit tests (T2T hub down or moved)

  jrobinso

  committed
  8f79f06

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• Bug fix -- copied clipped sequences were reverse complemented for (-) strand alignments. This is inconsistent with copy read sequence, and the SAM/BAM conventions. Fixes igvteam#1487

  jrobinso

  committed
  df442b9

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• account for alignment strand in MM validation. See issue igvteam#1476

  jrobinso

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  bc3addc

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Commits on Feb 7, 2024

• Simplify gct probe mapping error message

  jrobinso

  committed
  52332ed

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• Remove "bam" files from ENCODE lists, they aren't indexed.

  jrobinso

  committed
  958c119

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• auto trim entries to track hub dialog. Fixes igvteam#1485

  jrobinso

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  f3444ed

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Commits on Feb 2, 2024

• validate base mod counts by default

  jrobinso

  committed
  dc0eb95

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Commits on Feb 1, 2024

• Turn base modes "group by strand" off by default. See igvteam#1478

  jrobinso

  committed
  2820304

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Commits on Jan 31, 2024

• Set validate basemod calls to off by default. See issue igvteam#1476

  jrobinso

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  a37413e

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• Update script message

  jrobinso

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  25baf75

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Commits on Jan 26, 2024

• rollback whitespace changes

  

  jrobinso

  authored and

  lbergelson

  committed
  3cd649c

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• Catch errors parsing supplementary alignments

  

  jrobinso

  authored and

  lbergelson

  committed
  d8a1fe7

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• Echo required version number in startup script.

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  5d0fe7b

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