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Commits on Mar 23, 2020

• release current tool (especially drag tool) in data panel on mouse release

  jrobinso

  committed
  71f8969

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• Add "group by phase"

  jrobinso

  committed
  df89164

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• ALign alignment and coverage tracks "zoom in notice" threshold.

  jrobinso

  committed
  0e1274b

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• CoverageTrack -- fix broken autoscale.

  jrobinso

  committed
  98dd034

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• Change in alignment arrow width calculation -- use total length of alignment on reference, not the length of the last (leftmost or rightmost) block.

  jrobinso

  committed
  dbebc00

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• Automatically group "linked" alignments if not otherwise grouped.

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  jrobinso

  committed
  d1fb3cd

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• Reroganize alignment preferences, popup menu

  jrobinso

  committed
  8396784

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Commits on Mar 22, 2020

• Remove problematic unit test. Tests that depend on Thread.sleep() are generally unreliable.

  jrobinso

  committed
  3900d3d

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• Fix problems with reload session

  jrobinso

  committed
  8f0b7aa

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• Link alignments by arbitrary tag. See issue igvteam#680

  jrobinso

  committed
  15d576e

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Commits on Mar 20, 2020

• Add sort alignments by readname. Fixes igvteam#419

  jrobinso

  committed
  0e6a0e3

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• linked read refactoring.

  jrobinso

  committed
  f95cb2c

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Commits on Mar 19, 2020

• AlignmentTrack cleanup -- reordering

  jrobinso

  committed
  bd88167

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• intellij code analysis

  jrobinso

  committed
  1779264

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Commits on Mar 17, 2020

• fix minor issues with "Reload Tracks" and "Reload Sessions".

  jrobinso

  committed
  1bc077e

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• Preference to set the size of the reference sequence extension for soft clips (i.e. soft clips extending beyond the ends of the reference). Previously this was hard coded to 1kb.

  jrobinso

  committed
  05cba1f

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• .

  jrobinso

  committed
  8b9e1f2

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• remove broken unit test

  jrobinso

  committed
  a42e6cc

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• GWAS refactoring

  jrobinso

  committed
  ba0dde1

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Commits on Mar 10, 2020

• Preference issues

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  jrobinso

  committed
  8d685b2

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Commits on Mar 8, 2020

• Add user feedback for alignment clustering when there aren't enough features to cluster.

  jrobinso

  committed
  261fccf

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Commits on Mar 7, 2020

• formatting & clean up

  jrobinso

  committed
  5af506c

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Commits on Mar 6, 2020

• Merge branch '2.8'

  jrobinso

  committed
  5a6fa5a

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• Merge remote-tracking branch 'origin/dev_2.9'

  jrobinso

  committed
  fd68c57

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• Refactor treatment of alignments with no read sequence -- highlight soft clips and mismatches based on cigar string (S and X).

  jrobinso

  committed
  4bfcb05

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• color soft clipped and mismatched blocks from cigar string when read sequence is null

  jrobinso

  committed
  57f8938

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• Refactoring and consolidation of alignment renderer methods.

  jrobinso

  committed
  1f30be8

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• formatting

  jrobinso

  committed
  a6b74b6

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Commits on Mar 4, 2020

• Rework reload session & tracks. Fixes igvteam#659

  jrobinso

  committed
  3572f69

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• Restore name (and other attributes) to coverage track on session restore. See issue igvteam#766.

  jrobinso

  committed
  c57f29d

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Commits on Feb 29, 2020

• bug fix -- gwas track names not displayed

  jrobinso

  committed
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Commits on Feb 22, 2020

• Show All Chrom view when search is "*" (igvteam#757)

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  amwenger

  and

  jrobinso

  authored
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Commits on Feb 20, 2020

• Fix AWS Glacier/Deep Archive loading of restored objects (igvteam#759)

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  brainstorm

  authored
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Commits on Feb 12, 2020

• Use native file dialog on MacOS for "igvtools" UI. Possibly fixes problem with Catalina.

  jrobinso

  committed
  b4a0e3d

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Commits on Feb 11, 2020

• git htsjdk from Maven

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  jrobinso

  committed
  ebe1273

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