Commits

Branch selector

 v2.2

User selector

All users

Datepicker

All time

Commit History

Commits on Mar 22, 2013

• Add 'transcript_id' to known nameFields for GFF

  Show description for 5ab1a1c
  jrobinso

  committed
  5ab1a1c

  Copy full SHA for 5ab1a1c

Commits on Mar 18, 2013

• Bug fix. TCGA auto-generated sample names not used.

  jrobinso

  committed
  3fcc28e

  Copy full SHA for 3fcc28e

Commits on Mar 17, 2013

• IGV-1896. The sampleID attribute of Resource elements was ignored when looking up attributes.

  jrobinso

  committed
  42a4c91

  Copy full SHA for 42a4c91

• IGV-1896. The sampleID attribute of Resource elements was ignored when looking up attributes.

  jrobinso

  committed
  0397103

  Copy full SHA for 0397103

Commits on Mar 14, 2013

• Goby - Fix possible IndexArrayOutOfBounds exception

  jrobinso

  committed
  c4dd5bc

  Copy full SHA for c4dd5bc

• Bug fixes:

  Show description for a062831
  jrobinso

  committed
  a062831

  Copy full SHA for a062831

Commits on Mar 13, 2013

• Account for insertions when sorting alignments "by base"

  jrobinso

  committed
  80cbd5e

  Copy full SHA for 80cbd5e

• Fix bug in GenomeSummaryData

  Show description for a8ddc74
  jrobinso

  committed
  a8ddc74

  Copy full SHA for a8ddc74

Commits on Mar 11, 2013

• Remove indiscriminate user of anti-aliasing.

  jrobinso

  committed
  5ad91d1

  Copy full SHA for 5ad91d1

Commits on Mar 10, 2013

• Adjust scale threshold at which insertions are shown.

  Show description for 98dd3ad
  jrobinso

  committed
  98dd3ad

  Copy full SHA for 98dd3ad

Commits on Mar 9, 2013

• Cufflinks support -- parse fpkm and gene_exp.diff files

  jrobinso

  committed
  1962f76

  Copy full SHA for 1962f76

• Bug fix -- precomputed coverage not shown in whole-genome view

  jrobinso

  committed
  cc19f70

  Copy full SHA for cc19f70

Commits on Mar 8, 2013

• Set autoscale to false when scale manually set

  

  Jacob Silterra

  committed
  89cc6cd

  Copy full SHA for 89cc6cd

• Modify build process to exclude certain jars from being unzipped

  Show description for b82a336
  

  Jacob Silterra

  committed
  b82a336

  Copy full SHA for b82a336

Commits on Mar 1, 2013

• Remove reference to "firstGenome" in IGVCommandBar. This was no longer being used, and can cause IGV startup to fail.

  jrobinso

  committed
  c3409a0

  Copy full SHA for c3409a0

Commits on Feb 26, 2013

• Fix for filter bug -- filtering removed feature tracks

  jrobinso

  committed
  1f0f750

  Copy full SHA for 1f0f750

Commits on Feb 19, 2013

• GFF bug fixes (1) missing features, (2) reading frame not set

  jrobinso

  committed
  9d5d153

  Copy full SHA for 9d5d153

Commits on Feb 15, 2013

• Make exome button option a user preference

  jrobinso

  committed
  1ebc54e

  Copy full SHA for 1ebc54e

Commits on Feb 13, 2013

• Fix bug in chromosome name comparison -- assumption that all numeric strings could be parses as an "int".

  jrobinso

  committed
  4883b5a

  Copy full SHA for 4883b5a

• Bug fix -- whole genome scores from TDF files are not shown even for "well known" genomes.

  Show description for 2dc3124
  jrobinso

  committed
  2dc3124

  Copy full SHA for 2dc3124

Commits on Jan 25, 2013

• Fix for IGV-1892, null pointer exception loading sessions with "merge" parameter

  jrobinso

  committed
  8bad607

  Copy full SHA for 8bad607

Commits on Jan 24, 2013

• Move IGV.repaint.... calls outside of synchronized blocks

  

  Jacob Silterra

  committed
  cd33d99

  Copy full SHA for cd33d99

Commits on Jan 23, 2013

• Add .seg.data.txt extension (for TCGA)

  jrobinso

  committed
  e55db8d

  Copy full SHA for e55db8d

Commits on Jan 17, 2013

• Move testWriteStdIn to newly created RuntimeUtilsTest

  Show description for 6d72a95
  

  Jacob Silterra

  committed
  6d72a95

  Copy full SHA for 6d72a95

• Update tests to reflect new method names and include test data.

  Show description for 6ab063f
  

  Jacob Silterra

  committed
  6ab063f

  Copy full SHA for 6ab063f

Commits on Jan 14, 2013

• Don't draw arrows for gene if there is no strand

  

  Jacob Silterra

  committed
  d1254aa

  Copy full SHA for d1254aa

• Add preference to disable anti-aliasing. Jira 1888

  jrobinso

  committed
  1702317

  Copy full SHA for 1702317

Commits on Jan 10, 2013

• Refine chrom order check for TDF files. The rules are now

  Show description for 706b031
  jrobinso

  committed
  706b031

  Copy full SHA for 706b031

Commits on Jan 9, 2013

• Fix for Jira-1866. All but last GFF header line was ignored.

  jrobinso

  committed
  16ab2ed

  Copy full SHA for 16ab2ed

• Fix for WG TDF problem -- hanging with large #s of samples. This fixes pushed computation of the wg data down a level, from TDFDataSource (one data source per track) to TDFReader (one reader per fi…

  Show description for 8c790e7
  jrobinso

  committed
  8c790e7

  Copy full SHA for 8c790e7

• Fix for WG TDF problem -- hanging with large #s of samples. This fixes pushed computation of the wg data down a level, from TDFDataSource (one data source per track) to TDFReader (one reader per fi…

  Show description for d75c7ee
  jrobinso

  committed
  d75c7ee

  Copy full SHA for d75c7ee

Commits on Jan 7, 2013

• removed old tribble jar

  jrobinso

  committed
  2eb18b6

  Copy full SHA for 2eb18b6

• tribble update

  jrobinso

  committed
  ca4f8e0

  Copy full SHA for ca4f8e0

• Tweak to TDF whole genome calculation -- properly weight values by bases covered. This really only matters for bins which span chromosomes.

  jrobinso

  committed
  f0b479e

  Copy full SHA for f0b479e

Commits on Jan 6, 2013

• Fix for whole-genome view problem with TDF. Many files are touched because of some method name changes for genome coordinates. The fix ignores prestored values for whole genome scores in the TDF fi…

  Show description for 16cb4e1
  jrobinso

  committed
  16cb4e1

  Copy full SHA for 16cb4e1

Pagination

Previous

Next