CHANGES IN VERSION 1.8.5
------------------------

BUG FIXES

   o Found a typo in the consensus to PPM calculation for the DNA ambiguity
     letter Y which resulted in incorrect PPM values.

CHANGES IN VERSION 1.8.4
------------------------

BUG FIXES

   o Fixed incorrect handling of the -alph parameter in run_meme() (reported
      by @Irenexzwen).

CHANGES IN VERSION 1.8.3
------------------------

BUG FIXES

    o Fixed improper handling of MEME version string in read_meme().

CHANGES IN VERSION 1.8.2
------------------------

BUG FIXES

    o Increase compliance with MEME motif format: motif files with missing
      alphabets/strand/bkg are now allowed and  will be assumed to be
      DNA/+/uniform frequencies. A check for the MEME version is performed,
      though only a warning is given if not found.

    o Fixed typo in run_meme() missing dependency error message.

CHANGES IN VERSION 1.8.1
------------------------

BUG FIXES

    o Fixed error when scan_sequences() is used with both RC = TRUE and
      calc.pvals = TRUE.

    o Fixed motif.i column in scan_sequences() results not reporting correctly
      when RC = TRUE.

    o Fixed memory access bug in motif_pvalue() when k was set to a value
      resulting in three or more submotifs.

CHANGES IN VERSION 1.8.0
------------------------

NEW FEATURES

    o scan_sequences()/enrich_motifs() can now be used to scan/enrich for
      gapped motifs. A new section has been added to the SequenceSearches.Rmd
      vignette.

    o scan_sequences(..., use.gaps), enrich_motifs(..., use.gaps): ignore motif
      gap information.

    o read_meme(), write_meme(): now fully support custom alphabets.

    o prob_match(), prob_match_bkg(): calculate the probability of a motif
      match based on background frequencies of the motif object or provided
      values, respectively.

    o enrich_motifs(), get_matches(), get_scores(), motif_pvalue(),
      motif_score(), scan_sequences(), score_match(): new allow.nonfinite
      parameter, allowing for the functions to work even if non-finite values
      are present in the motif PWM.

    o read_matrix(..., comment): allows for comments to be ignored in motif
      files.

    o write_matrix(..., digits): control the number of digits to use for
      writing motif positions.

    o New mask_seqs() utility function: inject hard masks into sequences.

    o scan_sequences(..., warn.NA), enrich_motifs(..., warn.NA): new option
      which can disable warnings from non-standard letters being detected
      in the input sequences.

    o get_bkg(..., window, window.size, window.overlap): new options for
      calculating sequence background in windows.

    o get_bkg(..., merge.res): new option to return background information for
      individual sequences.

    o scan_sequences(..., calc.pvals): new option to calculate P-values for
      sequence hits. This is merely automating using the results from
      scan_sequences() to calculate P-values manually with motif_pvalue().

    o view_motifs(..., show.positions, show.positions.once, show.names): new
      options for customizing the look of plotted motifs.

MINOR CHANGES

    o read_matrix(..., positions): added partial argument matching.

    o create_sequences(), shuffle_sequences(), motif_pvalue(): the c++ random
      engine has been changed from std::default_random_engine to std::mt19937.
      This should allow for the same rng.seed value to result in the same
      output regardless of OS.

    o score_match() has been vectorized (alongside new prob_match() function).

    o The ape and ggtree packages are now no longer imported and must be
      installed seperately in order to use motif_tree().

    o The processx package is no longer imported and must be installed
      seperately in order to use run_meme().

    o The pseudocount slot is now shown when universalmotif class objects are
      printed.

    o get_bkg(): the list.out and as.prob options have been disabled. To
      simplify the function, the only possible output (exception: if to.meme is
      not NULL) is a DataFrame showing both counts and probabilities.

    o Changed the default look of motifs plotted by view_motifs().

    o General documentation cleanup.

BUG FIXES

    o Changing motif backgrounds with `[<-` will now make sure to set correct
      vector names.

    o get_bkg() will now correctly ignore non-standard letters and letters
      missing from the provided alphabet during counting.

CHANGES IN VERSION 1.6.4
------------------------

BUG FIXES

    o cbind(): do not ignore the pseudocount slot.

    o Fixed typo in IntroductionToSequenceMotifs.Rmd.

    o Fixed U() function in IntroductionToSequenceMotifs.Rmd, no longer returns
      NA values if 0s are present.

    o read_cisbp(): no parsing errors for motifs with missing/partial header
      info.

CHANGES IN VERSION 1.6.3
------------------------

BUG FIXES

    o scan_sequences(): commented out WIP code for scanning gapped motifs.

CHANGES IN VERSION 1.6.2
------------------------

BUG FIXES

    o motif_tree(): 'daylight' layout is no longer disabled.

CHANGES IN VERSION 1.6.1
------------------------

BUG FIXES

    o summarise_motif(): properly retrieves altname slot. Contribution from
      Spencer Nystrom (https://github.com/bjmt/universalmotif/pull/9).

    o read_meme(): for LIKE type alphabets, make sure PROTEIN-LIKE is
      understood as being AA.

CHANGES IN VERSION 1.6.0
------------------------

NEW FEATURES

    o log_string_pval(): small utility function to obtain the log of
      string-formatted p-values (such as those often carried in
      MEME-formatted motifs which are smaller than R's double.xmin limit).
      Likely only a temporary solution.

    o view_motifs(..., return.raw) option: instead of returning a plot
      type object, return the aligned motif matrices.

    o view_motifs(..., dedup.names) option: allows plotting of motifs with
      duplicated names by appending a unique string.

    o merge_motifs(..., new.name) option: assign a name to the new merged motif
      instead of collapsing the names of the merged motifs together.

    o round_motif() utility: round down very low letter-position scores to
      zero.

MINOR CHANGES

    o Removed most previously deprecated function arguments.

    o Make sure view_motifs(..., use.type = "ICM") properly sets ylim.

    o create_motif(): single motif positions can now be created.

    o create_motif(), character input: nsites slot is left empty is input is
      a single string. It is still filled if the input consists of multiple
      strings.

    o merge_motifs(): ALLR/ALLR_LL/KL/IS methods no longer add pseudocounts to
      the motifs. Instead, pseudocounts are added to temporary internal copies
      which are used for comparison and alignment. The original un-modified
      matrices are then combined.

    o read_meme(): now supports DNA-LIKE, RNA-LIKE, and AA-LIKE alphabets,
      though these will be treated as regular DNA, RNA, and AA alphabets,
      respectively. Contribution from Spencer Nystrom
      (https://github.com/bjmt/universalmotif/pull/7).

    o Some cleanup to documentation and vignettes.

    o General code cleanup.

BUG FIXES

    o write_meme() now includes altname slot if filled. Contribution from
      Spencer Nystrom (https://github.com/bjmt/universalmotif/pull/5).

    o write_meme() checks for and removes any spaces/equal signs in motif
      names/altnames.

    o view_motifs(..., use.type = "ICM"): check for zero IC motifs, as these
      cannot be plotted by ggseqlogo.

CHANGES IN VERSION 1.4.10
-------------------------

BUG FIXES

    o Updated the warning from v1.4.9 to make users aware that the daylight
      layout will be permanently disabled for Bioconductor 3.10.

CHANGES IN VERSION 1.4.9
------------------------

BUG FIXES

  o Temporarily disabling the 'daylight' layout for motif_tree() to get
    around a new bug.

CHANGES IN VERSION 1.4.8
------------------------

BUG FIXES

    o Fixed buffer overflow error in motif_peaks().

CHANGES IN VERSION 1.4.7
------------------------

BUG FIXES

    o Fixed dangling references in compare_motifs_helper.cpp and
      utils-exported.cpp.

    o Trying to subset a motif to a single column no longer throws an error.

CHANGES IN VERSION 1.4.6
------------------------

BUG FIXES

    o scan_sequences(): will now actually emit a warning when non-standard
      letters are detected.

CHANGES IN VERSION 1.4.5
------------------------

BUG FIXES

    o run_meme(): don't try and delete R's tempdir.

CHANGES IN VERSION 1.4.4
------------------------

BUG FIXES

    o Minor fix to how args are fed to processx::run() in run_meme().

CHANGES IN VERSION 1.4.3
------------------------

BUG FIXES

    o Suppress message output from library(TFBSTools) call in
      MotifManipulation.pdf vignette preamble code.

CHANGES IN VERSION 1.4.2
------------------------

BUG FIXES

    o Stopped using BiocStyle, as a current bug was preventing the package from
      building successfully.

CHANGES IN VERSION 1.4.1
------------------------

BUG FIXES

    o When using create_motif() with an AAStringSet object, amino acid letters
      will now be properly sorted and match the motif rows.

CHANGES IN VERSION 1.4.0
------------------------

NEW FEATURES

    o scan_sequences(..., threshold.type) option: 'logodds.abs'. Allows
      the exact threshold scores to be provided.

    o compare_motifs() option: 'min.position.ic'. Prevent low-IC positions in
      an alignment from contributing to the final alignment score.

    o compare_motifs() option: 'score.strat'. Instruct the function how to deal
      with individual column scores in an alignment. This is also replaced
      the old way of choosing between sum and mean via prepending an 'M' to the
      metric name. Strategies for combining column scores include: sum,
      arithmetic mean, geometric mean, median, Fisher Z-transform, and weighted
      means.

    o Motif comparison metrics: average log-likelihood ratio, squared Euclidean
      distance, Hellinger distance, Bhattacharyya coefficient, Manhattan
      distance, lower limit average log-likelihood ratio, weighted Euclidean
      distance, weighted Pearson correlation coefficient.

    o compare_columns() utility: Compare two 1d numeric vectors using the
      comparison metrics from compare_motifs().

    o compare_motifs() option: 'output.report'. Generate an output report when
      'compare.to' is provided, showing motif alignments of top matches.

    o get_scores() utility: Extract all possible scores from a motif.

    o filter_motifs(): Filter using the 'extrainfo' slot.

    o MotifComparisonAndPvalues.pdf vignette: the comparisons and P-values
      sections have been moved from AdvancedUsage.pdf to their own vignette.
      Higher order motifs, enrichment and run_meme() usage sections have been
      moved to SequenceSearches.pdf.

MINOR CHANGES

    o Removed 'random' shuffling method.

    o Using RcppThread instead of BiocParallel in several functions:
      compare_motifs(), create_sequences(), get_bkg(), motif_pvalue(),
      scan_sequences(), shuffle_sequences(). This means parallelization can
      occur within C++ code which is much faster than having to jump between
      R and C++. Currently motif_peaks(), read_motifs() and write_motifs()
      are the only remaining functions which offer optional BiocParallel
      usage.

    o Many performance improvements to functions relying on internal C++ code.
      Several internal R functions have been replaced with C++ versions.

    o Changed behaviour of make_DBscores() and motif comparison P-values.
      Re-calculated internal P-value databases.

    o For merge_motifs(..., use.type): now only accepts 'PPM'.

    o When comparing all motifs to all motifs with any method in
      compare_motifs(), the diagonal entries now properly show the max/min
      possible similarity/distance scores.

    o New internal merge_motifs() implementation. This also fixes a previous bug
      with incorrect PPM averaging.

    o read_homer(): the logodds score is converted to a P-value.

    o motif_pvalue(): New score calculator. Exact scores are still calculated
      the same (but with a faster C++ function), but approximate scores are
      now calculated by randomly generating score distributions from size 'k'
      motif score blocks.

    o motif_pvalue(): Added a safety check when trying to use this function
      with large motifs. Will throw a warning when nrow(matrix)^k > 1e8 and
      reduce k accordingly before continuing.

    o Adjusted P-value calculation in motif_peaks() to not display Pval = 0
      so easily by instead estimating a normal distribution from random peaks.

    o convert_type(): make sure not to leave any zeros in bkg vector when a
      pseudocount greater than zero is used.

    o enrich_motifs(): split up 'hits' and 'positional' resuts into their own
      data.frames.

    o Replaced several instances of cat() with message() for printing progress
      updates.

    o Positional tests have been removed from enrich_motifs(). See
      motif_peaks() for testing motif-sequence positional preferences.

    o In read_meme(): E-values are now additionally stored in the extrainfo
      slot. This is to preserve E-values smaller than the R double precision
      limit.

    o In read_transfac(): Matrix values are rounded, to prevent errors when
      reading in matrices with non-integers.

    o Update JASPAR2018_CORE_DBSCORES with new compare_motifs() methods and
      params.

    o universalmotif print() method now returns the object invisibly,
      instead of NULL.

BUG FIXES

    o read_meme() will now properly parse background letter frequencies which
      span more than one line.

    o convert_motifs() will not error-out when trying to convert a PFMatrix
      with a family character vector longer than one.

    o Fixed P-value calculation when importing HOMER motifs. Peviously it
      would simply assume the log threshold value was the P-value. Now
      motif_pvalue() is used to properly calculate a P-value.

CHANGES IN VERSION 1.2.1
------------------------

BUG FIXES

    o Mispelled variable in enrich_motifs().

CHANGES IN VERSION 1.2.0
------------------------

NEW FEATURES

    o New motif_peaks() function: test for significantly overrepresented peaks
      of motif sites in a set of sequences.

    o New get_bkg() function: calculate background frequencies of sequence
      alphabets, including higher order backgrounds. Works for any sequence
      alphabet. Can also create MEME background format files.

    o read_meme() has a new option, readites.meta, which allows for reading
      individual motif site positions and P-values, as well as combined
      sequence P-values.

    o shuffle_sequences(..., method = "markov") works for any set of
      characters instead of just DNA/RNA.

    o shuffle_sequences(): new shuffling method, 'euler'. This allows for k>1
      shuffling that preserves exact letter counts, as opposed to 'markov'.
      This method is set as the new default shuffling method.

    o create_sequences() has a new option "freqs" which allows for generating
      sequence from higher order backgrounds and any sequence alphabet
      (options "monofreqs", "difreqs" and "trifreqs" are now deprecated).

    o universalmotif objects can now hold onto higher order backgrounds.

    o motif_pvalue() with use.freq > 1 can calculate P-values from
      provided higher-order backgrounds, instead of assuming a uniform
      background.

    o add_multifreq() adds corresponding higher order background probabilities
      to motifs.

    o New get_klets() utility function: generate all possible k-lets for any
      set of characters.

    o New score_match() utility function: score a match for a particular motif.

    o New get_matches() utility function: get all possible motif matches above
      a certain score.

    o New count_klets() utility function: count all k-lets for any string
      of characters.

    o New motif_score() utility function: calculate motif score from input
      thresholds.

    o New shuffle_string() utility function: shuffle a string of character
      using one of three methods: euler, linear, and markov.

    o The native write_motifs()/read_motifs() universalmotif format is now
      YAML based. Motifs written before v1.2.0 can still be read by
      read_motifs().

MINOR CHANGES

    o Increased input security for character type parameters throughout.

    o Expanded motif_pvalue(), scan_sequences(), motif_tree() examples
      sections.

    o New vignette sections for motif_peaks() and get_bkg() added to
      SequenceSearches.Rmd.

    o Various vignette tweaks.

    o Fixed various spelling mistakes throughout, added Language field to
      Description, and added spell check to tests.

    o Documentation for the "random" shuffling method has been removed and a
      warning is shown when used to tell the user that it will be removed in
      the next minor update.

    o Generally increased test coverage.

    o The "k=1", "linear" and "markov" shuffling methods are much faster.

    o create_sequences() for higher order backgrounds is much faster.

    o Faster add_multifreqs(): slight improvement for DNA motifs, big
      improvement for non-DNA motifs.

    o sample_sites() has been rewritten for use.freq > 1: the probability of
      each letter in the site is now dependent on the previous letters (also
      faster and more memory efficient for any use.freq).

    o Improvement to calculating motif scores from p-value input: no
      longer guesses different scores, instead estimating a normal distribution
      of scores. This new approach is much, much faster and more memory
      efficient. It does however assume a uniform background.

    o The "score.pct" column in scan_sequences() results now represents the
      percent score based on the total possible score, not just the score
      between zero and the max possible score.

    o summarise_motifs() is much faster.

    o Objects in data/ are saved using serialization format version 3.

    o convert_motifs(motif, class = "universalmotif-universalmotif"): performs
      a validObject() check if "motif" is a universalmotif object.

    o The show() method for universalmotif objects performs a validObject()
      check first.

    o motif_rc() has a new option "ignore.alphabet", used to turn on or off the
      alphabet check (checks for DNA/RNA motif).

    o Added "overwrite" and "append" options to write_*() functions.

    o enrich_motifs(..., return.scan.results = FALSE): uses a slimmed down
      version of scan_sequences() which skips construction of the complete
      results data.frame, saving a tiny bit of time on large jobs.

    o compare_motifs() now includes log P-values. This way comparisons can
      still be properly ranked even if their P-values are below the machine
      limit.

    o convert_motifs() from MotifList (MotifDb) carries over dataSource.

    o If a MEME motif has two names, the second will be assigned as "altname"
      by read_meme().

    o Utilities documentation has been split into two: ?utils-motif and
      ?utils-sequence.

BUG FIXES

    o Fixed IC score calculation from character input in create_motif().

    o The internal DNA consensus letter calculation previously did not assign
      ambiguous letters when one PPM position was >0.5 and another was >0.25.
      This was unintended behaviour and will now output the proper ambigous
      DNA letter.

CHANGES IN VERSION 1.0.22
-------------------------

BUG FIXES

    o Fixed incorrect RcppExports code introduced in last patch.

CHANGES IN VERSION 1.0.21
-------------------------

BUG FIXES

    o Fixed an incorrect citation in motif_pvalue().

CHANGES IN VERSION 1.0.20
-------------------------

BUG FIXES

    o Fixed a bug introduced in previous patches where create_sequences()
      fails with alphabet = "RNA" and missing difreq/trifreq.

CHANGES IN VERSION 1.0.19
-------------------------

BUG FIXES

    o Fixed create_sequences(alphabet = "RNA") when providing difreq/trifreq.

CHANGES IN VERSION 1.0.18
-------------------------

BUG FIXES

    o Fixed alphabet letters being stripped from difreq and trifreq params in
      create_sequences().

    o Fixed an incorrect call to sample() when using create_sequences() with
      difreq.

CHANGES IN VERSION 1.0.17
-------------------------

BUG FIXES

    o Custom motif alphabets are properly sorted in the alphabet slot of motifs.

    o scan_sequences() properly matches custom sequence and motif alphabets.

CHANGES IN VERSION 1.0.16
-------------------------

BUG FIXES

    o scan_sequences() will now properly create a scoring matrix from motifs
      with pseudocounts of 0.

CHANGES IN VERSION 1.0.15
-------------------------

BUG FIXES

    o view_motifs() will now give an informative error message when trying
      to plot multiple motifs with non-unique names.

CHANGES IN VERSION 1.0.14
-------------------------

BUG FIXES

    o Fixed 'method' parameter documentation for motif_tree().

CHANGES IN VERSION 1.0.13
-------------------------

BUG FIXES

    o Fixed the error message given when a vector of incorrect length is
      used in a function.

CHANGES IN VERSION 1.0.12
-------------------------

BUG FIXES

    o motif_pvalue() no longer throws an error for
      motif_pvalue(..., pvalue = 0).

    o motif_tree() now works properly with dist objects as input.

CHANGES IN VERSION 1.0.11
-------------------------

BUG FIXES

    o The compare_motifs() example for min.mean.ic in the Advanced Usage
      vignette now makes more sense.

CHANGES IN VERSION 1.0.10
-------------------------

BUG FIXES

    o More strangely behaving MotifDb vignette code addressed in Advanced Usage
      vignette.

CHANGES IN VERSION 1.0.9
------------------------

BUG FIXES

    o shuffle_motifs() now produces motifs of proper length.

CHANGES IN VERSION 1.0.8
------------------------

BUG FIXES

    o Trying to prevent R CMD BUILD from changing the behaviour of vignette
      code involving MotifDb package.

CHANGES IN VERSION 1.0.7
------------------------

BUG FIXES

    o merge_motifs() will not show repeat families/organisms in new merged
      motif.

    o show method will no longer show name slot instead of altname.

CHANGES IN VERSION 1.0.6
------------------------

BUG FIXES

    o If MEME motif file has no strand info, assume `strand = "+"`, not
      `strand = c("+", "-")`.

CHANGES IN VERSION 1.0.5
------------------------

BUG FIXES

    o `read_meme()` can now read non-DNA/RNA motifs.

    o Removed duplicate line in run_meme.R.

    o `scan_sequences()` will not scan mismatching motif/sequence alphabets.

    o Verbose output from `scan_sequences()` will now display correctly.

    o Using `enrich_motifs()` and not finding any motif hits in the input
      sequences no longer throws an error.

    o Fixed threshold calculation in `enrich_motifs()`.

    o `enrich_motifs()` will now show results for motifs which have hits in
      target sequences but none in bkg sequences.

CHANGES IN VERSION 1.0.4
------------------------

BUG FIXES

    o Can now use `view_motifs(..., tryRC=F)` without throwing an error.

CHANGES IN VERSION 1.0.3
------------------------

BUG FIXES

    o Missed a couple [Biostrings::*StringSet-class] from last patch.

    o Updated README to reflect new installation method.

    o Wrapped instances of \link{} with \code{\link{}}.

CHANGES IN VERSION 1.0.2
------------------------

BUG FIXES

    o `read_meme()` can now read meme result files with missing strand info.

    o Use \link{*StringSet} instead of [Biostrings::*StringSet-class] in
      documentation.

    o No longer load MotifDb package in examples on Windows.

CHANGES IN VERSION 1.0.1
------------------------

BUG FIXES

    o TFBSTools motifs with multiple species can convert to universalmotif.

    o `scan_sequences()`: will now ignore non-standard letters instead of
      crashing.

CHANGES IN VERSION 1.0.0
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Changed the appearance of some of the vignette code blocks.

    o More documentation added in data.R.

BUG FIXES

    o Replaced for loop with `lapply()` in add_multifreq.R L120-133.

    o Replaced for loop with `lapply()` in enrich_motifs.R L327-330.

    o Replaced for loop with `lapply()` in shuffle_motifs.R L77-80.

    o Using `diag()` instead of for loop in `fix_pcc_diag()`
      (compare_motifs.R).

    o Fixed `read_motifs()` not parsing alphabet correctly.

    o Vignettes are now built using pdflatex instead of lualatex.

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

    o Ready for bioconductor.

CHANGES IN VERSION 0.98.0
-------------------------

    o Pre-bioconductor.
