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Commits on Oct 19, 2016

• Merge branch 'hotfix/2.3.6'

  dpryan79

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• plotHeatmap --yMin ... doesn't work, apparently because --yMin and --yMax are taken as strings and not converted to np.float64s. We can manually do that.

  dpryan79

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Commits on Oct 18, 2016

• Fix xml, which was already done in develop

  dpryan79

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• Try to fix #436

  dpryan79

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Commits on Sep 19, 2016

• Merge branch 'hotfix/2.3.5'

  dpryan79

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• Fix minor issue with the last commit, though in practice this will never be an issue

  dpryan79

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• Fix deeptools --version for 2.3.5

  dpryan79

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Commits on Sep 13, 2016

• RTD shouldn't show =False for boolean store_true options

  dpryan79

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Commits on Sep 12, 2016

• Incorrectly labeled the plotEnrichment documentation

  dpryan79

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• Revert "Allow bamCompare with the SES method to be completely --region aware, which might be bad if someone specifies anything smaller than a chromosome"

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  dpryan79

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• Allow bamCompare with the SES method to be completely --region aware

  dpryan79

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• Merge pull request #420 from j-andrews7/patch-1

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  dpryan79

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Commits on Sep 9, 2016

• Mention python3 support.

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  j-andrews7

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Commits on Sep 7, 2016

• Copy over the plotEnrichment documentation, which was added to the wrong branch before.

  dpryan79

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• Try fixing #417 for the 2.3.5 bugfix release

  dpryan79

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Commits on Sep 2, 2016

• Fix plotCoverage, which also wasn't python3 compatible with --outRawCounts

  dpryan79

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• Right, need to open the file first

  dpryan79

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• Fix #416, which is like #407 but python3-specific

  dpryan79

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• Fix #416

  dpryan79

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• Update CHANGES.txt

  dpryan79

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• Fix #413, --nanAfterEnd

  dpryan79

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• Fix #415, which was a Galaxy wrapper bug. Also, update all versions to 2.3.5

  dpryan79

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Commits on Aug 23, 2016

• Merge branch 'hotfix/2.3.4'

  dpryan79

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• Add a readthedocs page for plotEnrichment, fixes #408

  dpryan79

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Commits on Aug 19, 2016

• Update CHANGES.txt

  dpryan79

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• Fix #405

  dpryan79

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• Fix #407

  dpryan79

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Commits on Aug 12, 2016

• Merge pull request #400 from fidelram/g2.3.3

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  bgruening

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Commits on Aug 11, 2016

• upgrade to version 2.3.3

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Commits on Aug 8, 2016

• Merge branch 'hotfix/typo'

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• Fix #399

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Commits on Jul 27, 2016

• Merge branch 'hotfix/2.3.3'

  dpryan79

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• We don't need to check > 0

  dpryan79

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• Add tests for is_proper_pair() and make it a static method (like in develop). plotEnrichment now uses the same method.

  dpryan79

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Commits on Jul 26, 2016

• The function to check proper pairing was wrong before. It returned false if the insert size was within the expected range!

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