NEWS

CHANGES IN 1.27.1
-----------------------

  * Suggest 'markdown' package in DESCRIPTION and utilize hg19 as default freeze where applicable.

CHANGES IN 1.19.0
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  * Drop forced strand conversion to '+' and makeGRanges with add strand as '*' if none was found.

CHANGES IN 1.11.1
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  * GenomicRanges package update adjustments & improved tests

CHANGES IN 1.9.0
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  * code spacing edits & GenomicRanges package update adjustments

CHANGES IN 1.7.1
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  * code spacing edits & namespace conflict fixes

CHANGES IN 1.5.1
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  * ggplot2 update bug fixes.

CHANGES IN 1.3.2
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  * fixed duplicated featureName column in getSitesInFeature when allSubjectCols
  is TRUE.

CHANGES IN 1.3.1
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  * replaced plyr with dplyr

CHANGES IN 1.1.1
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  * added allSubjectCols & overlapType params to getSitesInFeature

CHANGES IN 0.99.9
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  * metadatacol bug fix

CHANGES IN 0.99.8
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  * plotdisFeature() obtains a geom parameter.

CHANGES IN 0.99.7
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  * Documentation fixes

CHANGES IN 0.99.6
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  * Using GRanges::sort in makeGRanges().

CHANGES IN 0.99.5
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  * Documentation changes.

CHANGES IN 0.99.4
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NEW FEATURES

  * plotdisFeature(), function to plot distance distribution to
    feature boundary.

  * Includes sites.ctrl dataset to compliment sites dataset.

CHANGES IN 0.99.3
-----------------------

NEW FEATURES

  * makeGRanges() inherits total functionality of makeRangedData() and an option
    to turn off factor to character conversion.

DEPRECATED AND DEFUNCT

	* Functions resizeRangedData() & makeRangedData() has been removed in favor
    of using only GenomicRanges-derived objects.

BUG FIXES

  * Improved seqinfo slot population method in makeGRanges()