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Commits on Dec 11, 2015

• Change name of method to fetch canonical chromosome name. Its been "backwards" forever and still trips me up, time to change.

  jrobinso

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Commits on Dec 10, 2015

• cram beginnings...

  jrobinso

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Commits on Dec 4, 2015

• Add chromosome size and alias files to repository

  jrobinso

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Commits on Nov 28, 2015

• Recognize gff version directives with major/minor numbers (e.g. ##gffVersion 3.2.1)

  jrobinso

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Commits on Nov 26, 2015

• GA4GH: try to guess chromosome naming convention if read query fails. Issue igvteam#181

  jrobinso

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  2e256bd

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• Fix broken unit test

  jrobinso

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• Added support for exporting splice junction features

  jrobinso

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Commits on Nov 25, 2015

• Fix NPE when exporting splice junction features

  jrobinso

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Commits on Nov 22, 2015

• Display error messages returned from google GA4GH posts. Fixes igvteam#181

  jrobinso

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Commits on Nov 19, 2015

• Fixes igvteam#177 - preferences set through port command not forcing refresh

  jrobinso

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Commits on Nov 8, 2015

• fix launch bug

  jrobinso

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Commits on Nov 7, 2015

• Remove LOS popup

  jrobinso

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Commits on Nov 3, 2015

• Force use of S3 download as opposed to Cloudfront for download of whole fasta files from Broad buckets

  jrobinso

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Commits on Oct 31, 2015

• Fix group autoscale logic

  jrobinso

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Commits on Oct 30, 2015

• autoscale bugs

  jrobinso

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Commits on Oct 29, 2015

• Disable group autoscale for production release

  jrobinso

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Commits on Oct 26, 2015

• Store group autoscale counter in session

  jrobinso

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Commits on Oct 25, 2015

• Add menu item for "group autoscale", active when multiple tracks are selected. Issue igvteam#25

  jrobinso

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• Added utility class for byte [] subarrays

  jrobinso

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Commits on Oct 24, 2015

• Bug fix -- base not shown in alignment popup if read sequence === ref sequence

  jrobinso

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• Combine "Load from URL" and "Load file and index from URL" menu items. See pull request igvteam#176

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Commits on Oct 23, 2015

• Remove feature track filter from Sashimi plots (filtered features without exons). Its confusing to see features in the IGV window and not in the Sashimi plot, and anyway why would we want to hide t…

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  jrobinso

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• Minor tweaks for pull request igvteam#176. Move "auto file discovery" cb from "Tracks" to "Advanced" tab. Add widget to JFormDesigner form to prevent it being removed upon code re-generation. Rever…

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Commits on Oct 22, 2015

• Bug fix -- data scale not drawn in coverage track

  jrobinso

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Commits on Oct 21, 2015

• Bug fix -- user defined gene lists were not editable

  jrobinso

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• Pull request merge

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Commits on Oct 20, 2015

• Partial fix for locked file handles, issue igvteam#77. This commit should fix non-indexed files.

  jrobinso

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• Fixes igvteam#177

  jrobinso

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  4fcde29

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• LOS support

  jrobinso

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Commits on Oct 19, 2015

• group autoscale

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Commits on Oct 17, 2015

• Autoscale groups of tracks - step 1

  jrobinso

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Commits on Oct 14, 2015

• paired end contact fix

  jrobinso

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Commits on Oct 12, 2015

• support for paired end contact calculation in igvtools

  jrobinso

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• interactin matrix

  jrobinso

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Commits on Oct 7, 2015

• Update to EqtlCodec

  jrobinso

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