NEWS

CHANGES IN VERSION 2.0.0
------------------------

NEW FEATURES

    * Better integration with Bioconductor API:
      - Added BiocParallel support for all parallel functions.
      - Propagate mcols() from GRanges, remove hard-coded column names, and
        limit use of data.frame objects.
      - Drop functionality such as readBed() and writeWiggle() already present
        in the rtracklayer package maintained by the Bioconductor core team.
    * polymeraseWave() is more reliable and has faster processing from several
      changes:
      - Parallel processing.
      - Less memory usage.
      - HMM calculations 10x faster not including parallel processing.
      - Genes are ignored if they have no reads within or nearby instead of
        blindly processing all annotated genes.
      - Errors from failure to fit distributions, etc are returned to the user
        via BiocParallel error handler bptry().

SIGNIFICANT USER-VISIBLE CHANGES

    * Remove functions:
      - readBed() and writeWiggle() reimplement rtracklayer import.bed(), and
        export.bw() / export.wig().
      - tlsDeming(), tlsLoess(), and tlsSvd() total least squares fit functions,
        commented as unreliable by the author and not used anywhere in the code
        base.
      - Redundant runMetaGene-like functions metaGeneMatrix() and metaGene_nL().
      - averagePlot() does not have a sufficiently broad use case.
    * Remove function arguments:
      - Broken NonMap/UnMAQ argument of polymeraseWave() and pausingIndex().
      - Buggy resampling arguments of getTxDensity().
      - Debug parameters from many functions.  For troubleshooting faults, it is
        much more informative to use debugonce(), browser(), etc per
        adv-r.had.co.nz and improve the now included unit tests.
    * Verbose flag now works for C functions.  The large volume of C messages
      can be silenced as originally intended instead of always being verbose.
    * Replace sweave package vignette with Rmd for easier user interaction.
      Less effort should be needed to maintain the vignette due to simpler
      syntax, and fewer obtuse LaTeX errors.
    * Disable default plotting of getTxDensity().  Only functions whose names
      start with 'plot' automatically generate plots.
    * getTxDensity() is faster and returns exact values instead of trapezoidal
      approximation.
    * windowAnalysis() now has no upper limit on stepSize.
    * polymeraseWave() returns GRanges instead of relative wave positions.
    * polymeraseWave() has a new within argument to find waves beyond annotated
      gene boundaries.

BUG FIXES AND IMPROVEMENTS

    * Fix windowAnalysis() "subscript out of bounds" error, and add corner case
      of empty ranges.  Fix regression of only returning single chromosome.
    * Fix corner cases of breakTranscriptsOnGenes() and combineTranscripts()
      failing when no break or join errors are detected.
    * Fix breakTranscriptsOnGenes() failing to validate assumption that
      annotations do not overlap (GitHub issue #2).
    * Fix polymeraseWave processing genes beyond chromosome boundaries and raise
      error when HMM fails to converge.
    * Fix makeConsensusAnnotations not correctly validating presence of gene ID
      column.  Additionally the gene ID column no longer uses the "gene_id"
      magic string and is configurable via the column argument.
    * One can now control makeConsensusAnnotations() parallelism.  Remove the
      hard coded 10 CPU cores.
    * Move all packages from Depends to Imports to fix Travis-CI bootstrap
      errors.
    * Add unit test suite using testthat:
      - All bugs discovered since version 1.7.0 now have corresponding
        regression tests.
      - Add lintr in unit tests to preserve code style.
    * New maintainer in response to dead upstream.
    * Add contributor instructions in README.
    * Add GitHub continuous integration using Travis-CI, covr, and codecov.
    * Fix R check errors, warnings and notes:
      - Fix RgammaMLE() namespace collision between R and C functions by
        renaming C function to Rgamma().
      - Add useDynamicSymbols removed by a previous maintainer in Bioconductor
        3.0.
    * Fix BiocCheck errors, warnings and notes:
      - Drop use of <<- from writeWriggle()
      - Indent at multiples of 4 spaces.
      - Wrap lines at 80 columns.


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