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Commits on Jun 20, 2014

• EQTL / Gtex updates

  jrobinso

  committed
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Commits on Jun 10, 2014

• Merge pull request igvteam#85 from broadinstitute/score_ignore_nans

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  jrobinso

  committed
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• If the only scores for a region are NaN, the region will be scored as NaN

  

  Jacob Silterra

  committed
  ae06c0e

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Commits on May 23, 2014

• Skip NaNs when calculating certain region scores

  

  Jacob Silterra

  committed
  b5b3ff0

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Commits on May 11, 2014

• Bug fix -- if any frames in "multi-locus" view had no alignments, alignments for all frames would be hidden. Bug was in packing logic.

  jrobinso

  committed
  95519bf

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Commits on May 10, 2014

• Correct popup text nomenclature

  jrobinso

  committed
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Commits on May 7, 2014

• Bug fix -- autoscale and log scale options incorrectly linked on coverage track

  jrobinso

  committed
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Commits on May 2, 2014

• Remove unused code

  jrobinso

  committed
  8e067b5

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• No longer truncate GFF attributes at 50 characters

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  Jacob Silterra

  committed
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Commits on Apr 23, 2014

• Null tests in alignment loading code

  jrobinso

  committed
  89ef61c

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Commits on Apr 17, 2014

• Add additional fields to VCF genotype tooltip text

  jrobinso

  committed
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Commits on Mar 21, 2014

• Add lookup table to allow change to preference keys

  jrobinso

  committed
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Commits on Mar 18, 2014

• Fix "index exists" test.

  jrobinso

  committed
  c10524b

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Commits on Mar 17, 2014

• Update na12878kb.jar to one built based on gsa-stable tag 3.0

  

  Jacob Silterra

  committed
  fa1c5f2

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• Update na12878kb.jar to one built based on gsa-stable tag 3.0

  

  Jacob Silterra

  committed
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Commits on Mar 14, 2014

• Make sure that Tribble index is used if one exists

  

  Jacob Silterra

  committed
  b70f10e

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• Account for the possibility of negative start coordinates when packing soft-clipped alignments

  jrobinso

  committed
  fbb0e8c

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• Fix gtf bug -- empty string id fields not handled properly

  jrobinso

  committed
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Commits on Mar 12, 2014

• Merge branch 'master' of github.com:broadinstitute/IGV

  

  Jacob Silterra

  committed
  dc368b3

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• Fix CombinedDataSource

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  Jacob Silterra

  committed
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• Initialize CombinedDataSourceDialog with 1st and 2nd track

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  Jacob Silterra

  committed
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• Init packing by getEnd, not getAlignmentEnd

  

  Jacob Silterra

  committed
  0ff6bd9

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• Fix alignment rendering but with "insert size & pair orientation" option

  jrobinso

  committed
  ff09e43

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• Enable "view mate region" in split screen for paired alignment view

  jrobinso

  committed
  88e3d20

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Commits on Mar 11, 2014

• Fix problem with cytoband parsing

  jrobinso

  committed
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Commits on Mar 4, 2014

• Fix for igv-help issue "IGV doesn't like fasta file", https://groups.google.com/forum/#!topic/igv-help/3X7EMCefH0U

  jrobinso

  committed
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Commits on Feb 27, 2014

• Fix bug in using buffer "overlap" in IGVSeekableBufferedStream, introduced in commit 178de52.

  jrobinso

  committed
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Commits on Feb 26, 2014

• Remove dependence on apache commons lang

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  Jacob Silterra

  committed
  358a00e

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• Replace goby jar with property

  

  Jacob Silterra

  committed
  8bf79e7

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• Fix version checking bug

  jrobinso

  committed
  e8a1aba

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• Add version check on startup

  jrobinso

  committed
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Commits on Feb 21, 2014

• Change sort order in fileHeader on SAM/BAM export

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  Jacob Silterra

  committed
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• Add more info to alignment writing error message

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  Jacob Silterra

  committed
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• Add error dialog if alignments cannot be output

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  Jacob Silterra

  committed
  edf394e

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Commits on Feb 20, 2014

• Fix typo in batik-codec file name

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  Jacob Silterra

  committed
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