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Commits on Feb 5, 2014

• Genbank updates: (1) if ACCESSION is blank or missing, use LOCUS for chr name. (2) allow gbk files to be loaded for feature definitions, ignoring fasta section.

  jrobinso

  committed
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Commits on Feb 3, 2014

• Change DBProfileEditor to be enabled in development mode

  

  Jacob Silterra

  committed
  a34ad53

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Commits on Jan 31, 2014

• Merge branch 'LoadFilesWithCommas'

  

  Jacob Silterra

  committed
  b7784d2

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Commits on Jan 30, 2014

• Fix bug where max zoom didn't properly recalculate when changing chromosome

  Show description for 8fe4622
  

  Jacob Silterra

  committed
  8fe4622

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Commits on Jan 28, 2014

• Added missing "Cursor" classes

  jrobinso

  committed
  1c2399a

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Commits on Jan 27, 2014

• Redo some logging

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  Jacob Silterra

  committed
  a2f2baa

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• Log to console during initialization of logging process

  

  Jacob Silterra

  committed
  60ff72b

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• Cursor project -- initial checking

  jrobinso

  committed
  e4eb86d

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Commits on Jan 23, 2014

• Whitespace/spelling/formatting changes

  

  Jacob Silterra

  committed
  c0d7d9b

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• Fix for loading bedgraph files with discontinuous chromosome data

  

  Jacob Silterra

  committed
  e87623d

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Commits on Jan 22, 2014

• Merge branch 'GlobalAlignmentPack'

  

  Jacob Silterra

  committed
  3689f45

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• Fix typo in createExomeBlockData method

  

  Jacob Silterra

  committed
  c06478a

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• Many tweaks to ExomeReferenceFrame

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  Jacob Silterra

  committed
  229f382

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• Fix cytoband rendering in Exome mode

  

  Jacob Silterra

  committed
  2c5c74a

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• Slight tweak to IGVFeatureRenderer so we don't do un-necessary calculations for null strand

  

  Jacob Silterra

  committed
  e222c06

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• Few changes to VariantReviewPlugin

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  Jacob Silterra

  committed
  ba910c2

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• Set anti-aliasing default to true for MacOS only. It doesn't seem to have much effect on other platforms, and reportedly causes performance issues on Linux.

  jrobinso

  committed
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Commits on Jan 21, 2014

• Don't add null buckets to map

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  Jacob Silterra

  committed
  f5d3255

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• Fix grouping key which was breaking all packing by groups

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  Jacob Silterra

  committed
  920eaec

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• Refactor packing

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  Jacob Silterra

  committed
  ebaf816

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• Minor bugfixes to packing

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  Jacob Silterra

  committed
  dffe3c7

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• Merge branch 'master' into GlobalAlignmentPack

  

  Jacob Silterra

  committed
  7a0b54c

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• Change method names in PositionCache

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  Jacob Silterra

  committed
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Commits on Jan 17, 2014

• Change logging statement when HEAD request fails

  

  Jacob Silterra

  committed
  090864f

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• Simplify PositionCache

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  Jacob Silterra

  committed
  9b6735a

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• Much refactoring of AlignmentPacker/Renderer

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  Jacob Silterra

  committed
  df7aca1

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• Cleanup.

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  Jacob Silterra

  committed
  83ce36b

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• Remove some unused elements from Row

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  Jacob Silterra

  committed
  2ef5d58

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• PositionMap -> PositionCache

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  Jacob Silterra

  committed
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Commits on Jan 16, 2014

• Have LRUCache use a hard reference for the map

  

  Jacob Silterra

  committed
  bf81e69

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• Modify LRUCache so we don't keep instance map

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  Jacob Silterra

  committed
  5536a19

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• When building list of IntervalLists for packing, make sure not to add duplicates

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  Jacob Silterra

  committed
  cde265f

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• Cache packed alignments by alignment range, not frame range

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  Jacob Silterra

  committed
  866c1d0

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• Use PositionMap to cache PackedAlignments

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  Jacob Silterra

  committed
  f49e860

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• Change AlignmentsCache -> PositionMap

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  Jacob Silterra

  committed
  e4c1ae4

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