CHANGES IN VERSION (1.3.1)
--------------------------

  o Updated CITATIOn with the published UMI4Cats paper.

CHANGES IN VERSION (1.1.10)
--------------------------

  o The vignette is updated with new examples showing the functionalities added
    in this new package version.
  o Fixed bug when bait is in the reverse strand and `sel_seqname` is set in 
    `getViewpointCoordinates()` (see issue #9).
  o Added function for plotting detected interactions with `callInteractions()`:
    `plotInteractions()` and `plotInteractionsUMI4C()`.
  o Added method for detecting significant interactions with the viewpoint using
    z-scores (`callInteractions()` and `getSignInteractions()`).
  o Added a function for combining restriction fragments that overlap a set of 
    query_regions (`combineUMI4C()`).
  o Create function for generating windows including a fixed number of fragments,
    allowing the use of sliding windows (`makeWindowFragments()`).
  o Added waldUMI4C() function for performing standard DESeq2 differential test 
    from raw UMIs. It allows providing `query_regions` for performing the test
    and summarizing the UMIs in the region by overlap (test each restriction
    fragment separately) or sum (sum UMIs from restriction fragments overlapping
    query regions).
    

CHANGES IN VERSION 1.1.9
--------------------------

  o Allow selection of number of reads to load from FastQ file in prep and split
    functions. Default: 1M reads (1e9).
  o Minor fixes BiocCheck.

CHANGES IN VERSION 1.1.8
--------------------------

  o Use `query_regions` to select the restriction fragments to use for differential
    testing in `diffWaldUMI4C`.    

CHANGES IN VERSION 1.1.7
--------------------------

  o Fixed bug with limits of the log2 OR values when plotting differential
    windows.


CHANGES IN VERSION 1.1.6
--------------------------

  o Fixed bug in creation of gene annotation when an exon belongs to more
    than one transcript.
  o Fixed bug when only one sample is provided (no name in assay columns).

CHANGES IN VERSION 1.1.5
--------------------------

  o Fixed bug in selection of reference UMI4C sample when more than 1 sample
    has the same number of total UMIs. Now it will select the first one.
    The selection of sample to use as reference can be overriden by the
    `ref_umi4c` argument.

CHANGES IN VERSION 1.1.4
--------------------------

  o Fixed bug in domainogram plotting where white color was not aligned
    with 0 log2 FC.

CHANGES IN VERSION 1.1.3
--------------------------

  o Fixed bug when providing a reference sample to use for normalizing UMI
    counts.

CHANGES IN VERSION 1.1.2
--------------------------

  o Fixed bug when `cut_pos`!=0 that generated a gap in the digested genome
    object (see issue #8)

CHANGES IN VERSION 0.99.21
--------------------------

  o Improvements in vignette and documentation.

CHANGES IN VERSION 0.99.20
--------------------------

  o Avoid duplication of fragment end calculation in plotDifferential for
    DESeq2 results.

CHANGES IN VERSION 0.99.19
--------------------------

  o Minor documentation changes to pass Bioconductor checks.


CHANGES IN VERSION 0.99.18
--------------------------

  o Fix DESeq2 example.
  o Reduce size of installed example tsv.gz count files.


CHANGES IN VERSION 0.99.17
--------------------------

  o Re-run example datasets and use again links from figshare.

CHANGES IN VERSION 0.99.16
--------------------------

IMPORTANT

  o This version is not compatible with the .tsv.gz files created by
    previous versions. You will need to run `contactsUMI4C()` again to generate
    updated .tsv.gz files.

UPDATES

  o Improved grouping arguments for UMI-4C objects: now creates a new UMI-4C
    object that can be accessed using `groupsUMI4C(umi4c)$condition`. This allows
    retaining replicate information in the main UMI4C object while allowing
    plotting grouped trends stored in `groupsUMI4C()`.

  o Added new statistical test using DESeq2: `differentialNbinomWaldTestUMI4C()`.

CHANGES IN VERSION 0.99.15
--------------------------

  o Fixed duplicated read number in read id (.singlePrepUMI4C) (see issue #5).
  o Changed example download urls to gattaca server.

CHANGES IN VERSION 0.99.14
--------------------------

  o Fixed bug where adaptive smoothed trend was normalized twice (see issue #4).

CHANGES IN VERSION 0.99.11
--------------------------

  o Uploaded example datasets urls in `downloadUMI4CexampleData()` to a more
    stable and permanent location (figshare.com).

CHANGES IN VERSION 0.99.10
--------------------------

  o Avoid running long and redundant examples, already tested in the vignette to
    avoid TIMEOUT build error.

CHANGES IN VERSION 0.99.9
--------------------------

  o Add data object `ex_ciita_umi4c` to use in examples and reduce check running
    times.

CHANGES IN VERSION 0.99.8
--------------------------

  o Update package vignette to clarify the origin of the different sample files
    used to exemplify a workflow using the UMI4Cats package.

CHANGES IN VERSION 0.99.7
--------------------------

  o Added unit tests using `testthat`.
  o Use BiocFileCache to download sample files.
  o Use tempdir() for demo purposes both in vignette and examples.
  o Added inst\scripts to describe how the sample data was generated.
  o Other minor changes to comply with Bioconductor review
    (see https://github.com/Pasquali-lab/UMI4Cats/issues/2#issue-637249954)

CHANGES IN VERSION 0.99.6
--------------------------

  o Delete downloaded and intermediate folders when building vignette.
  o Added `UMI4Cats_index` to .Rbuildignore to prevent ERRORs and
    WARNINGs in BioCCheck.

CHANGES IN VERSION 0.99.5
--------------------------

  o Increased speed of `getViewpointCoordinates()` by allowing pre-selection
    of viewpoint chromosome using `sel_seqname` argument.
  o Added reduced fastq files in extdata and allow downloading of reduced
    bowtie index to increase vignette building speed.

CHANGES IN VERSION 0.99.4
--------------------------

  o Added `.Rproj` files to .gitignore

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

  o Changed example in vignette and manuals to *CIITA*.
  o Added viewpoint name in `plotTrend()`.
  o Improved multi-panel plotting of `plotUMI4C()`.

CHANGES IN VERSION 0.99.2
--------------------------

  o Allow `ref_umi4c` to be used as reference for plotting colors, domainogram
    and differential analysis (not only for normalization).
  o Fixed error when using `sampleID` as `grouping` variable in `makeUMI4C()`.
  o Fixed bug in `results()` when `fomat=data.frame` and `ordered=TRUE`.
  o Improved visualization of differential regions reconverting `Inf` and `-Inf`
    to maximum and minimum (respectively) odd's ratio values.
  o Add more functionality details in the `Analyzing UMI-4C data with UMI4Cats`
    vignette.

CHANGES IN VERSION 0.99.1
--------------------------

  o Fixed error in function `createGeneAnnotation` and `plotGenes` that occurs
    when there are no genes in the region or a gene has multiple identifiers.
  o  Fixed duplicated generics definition for `SummarizedExperiment` objects to
    avoid error when reloading the package.
  o Fixed error when `bait_exclusion` is set to 0.
  o Added possibility to specify the sample to use as reference for normalization
    (`ref_umi4c` argument in `makeUMI4C`).
  o Now the `grouping` variable in `makeUMI4C()` is used more upstream in the
    analysis. For using different grouping variables, user must create different
    `UMI4C` objects.
  o Fixed bug where sometimes bait coordinates in the output tsv file are `NA`.
  o `statsUMI4C` now also outputs a stats summary table in `wk_dir/logs/stats_summary.txt`.
  o Improve function documentation.
  o Improve pkgdown UMI4Cats site.
  o Rewrite and improve the `Analyzing UMI-4C data with UMI4Cats` vignette.

CHANGES IN VERSION 0.99.0
--------------------------

  o First public release of UMI4Cats.
  o Added a `NEWS.md` file to track changes to the package.
