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Commits on Jun 15, 2022

• Apply "group by" menu option to selected alignment track only, not all alignment tracks. Fixes igvteam#1045

  jrobinso

  committed
  b0fc0b7

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• Fix bug in GFF parser.

  jrobinso

  committed
  006779a

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• Update to htsjdk 3.0.0 which includes support for cram reading using a subset of the reference.

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  lbergelson

  authored and

  jrobinso

  committed
  d67900f

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• fix unit test

  jrobinso

  committed
  3ca340b

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• Improvements to "bigRmsk" parsing.

  jrobinso

  committed
  f7603de

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Commits on Jun 14, 2022

• bug fix -- account for bigbed with no autosql

  jrobinso

  committed
  112b97e

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• add special codec for "bigRmsk" format

  jrobinso

  committed
  5cdc590

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• Fixes igvteam#1151 (group-by-strand broken in collapsed mode)

  jrobinso

  committed
  6b5d8d4

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Commits on Jun 13, 2022

• option in preferences to enable paired end mode by default

  

  ssadedin

  authored and

  jrobinso

  committed
  38a45bf

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• Increase number and length of lines to show in popup text

  jrobinso

  committed
  4125444

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• Create hyperlinks for feature attribute values that start with "https://"

  jrobinso

  committed
  0114505

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• Bug fix -- LittleEndianInputStream.readString() fails for certain character codes, specifically when code cast to byte would result in a negative number.

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  jrobinso

  committed
  d6e4948

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Commits on Jun 8, 2022

• null chromosome check

  jrobinso

  committed
  2749597

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Commits on Jun 6, 2022

• Prevent jumping beyond end of chromosome. Fixes igvteam#1150

  jrobinso

  committed
  3e47018

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Commits on Jun 3, 2022

• .

  jrobinso

  committed
  0bad46b

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Commits on Jun 1, 2022

• Add some logging to "BaseModification"

  jrobinso

  committed
  763c6e5

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• bisulfite sequencing -- small refactor for clarity

  jrobinso

  committed
  461d7f8

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Commits on May 31, 2022

• Support loading sessions (xml files) from AWS S3 file picker.

  jrobinso

  committed
  abf1379

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• Fix URLDecoder.decode call in anticipation of JDK 17. Fixes igvteam#1147

  jrobinso

  committed
  c03fea1

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Commits on May 26, 2022

• Support special property "id" as a feature label field.

  jrobinso

  committed
  ac0a462

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• use currently displayed name in feature info URLs

  jrobinso

  committed
  446b15d

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• suport feature info URL from json genome definitions

  jrobinso

  committed
  9572765

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• Allow specification of property / attribute for feature names. Fixes igvteam#1089

  jrobinso

  committed
  b1b0824

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Commits on May 25, 2022

• fix unit test

  jrobinso

  committed
  6fa75bf

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• .

  jrobinso

  committed
  80f67f7

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• BigBed parsing -- parse attribute names, improve popup text

  jrobinso

  committed
  7b2c6a9

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• * Remove unneccessary methods from IGVFeature interface -- getType(), getIdentifier(), setStart(), and setEnd()

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  jrobinso

  committed
  07b2059

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• remove unneccessary "getDescription" for IGVFeature interface

  jrobinso

  committed
  fa2c9c0

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• change IGVFeature attbitue interface to allow non-map based attribute collections

  jrobinso

  committed
  13fff05

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• Port uses of MultiMap -> Map for feature attributes.

  jrobinso

  committed
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Commits on May 16, 2022

• Update README

  jrobinso

  committed
  fcc9779

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• Update preferences.tab

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  helgathorv

  authored
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Commits on May 13, 2022

• preference wording...

  jrobinso

  committed
  7fb7326

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• Implement "fit to feature" for F/B hotkey feature jumping, with optional padding. Padding is in bp if > 0, or percentage if < 0, consistent with "go to" options.

  jrobinso

  committed
  8910719

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Commits on May 10, 2022

• Change selection criteria for panels -- if a track is not an annotation track (FeatureTrack) it goes in the top ("data") panel.

  jrobinso

  committed
  6c16148

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