chicane v0.1.8                                                  2021-11-03
--------------------------------------------------
* graceful handling of Gviz-UCSC error when retrieving chromosome lengths in vignettes
  when using R-4.1.0

chicane v0.1.7                                                  2021-09-20
--------------------------------------------------
* enabling future compatability with data.table v1.14.2 by changing syntax
 names(data.table)['x' == names(data.table)] <- 'y' to setnames(data.table, 'x', 'y')

chicane v0.1.6                                                  2021-07-20
--------------------------------------------------
* updated vignettes' section: Pre-processing data to detail creation of baitmap and fragments
  files and brought the naming of files in sync with Nature Protocols' paper
* fixed rare cases where scientific notations (e.g 1e10) were introduced in read.bed()
* fixed a typo in vignettes: create.standard.format to convert.standard.format

chicane v0.1.5							2021-06-08
--------------------------------------------------
* fixed prepare_bam.sh to make it work with all POSIX-compliant shells

chicane v0.1.4							2021-03-17
--------------------------------------------------
* fixed rare cases where scientific notations were introduced in convert2bed leading to 
 failure in bedr which treats it as a string (e.g 1e10)

chicane v0.1.3							2020-09-19
--------------------------------------------------
* fixed a bug with first distance bin when it contained self-ligated interactions
 with distance=0
* added log-likelihood statistics to rootograms and saved model fit statistics

chicane v0.1.2							2020-06-09
--------------------------------------------------
* added create.locus.plot function
* added create.standard.format function
* activated verbose statements
* add replicate comparison

chicane v0.1.1							2019-09-23
--------------------------------------------------
* improved memory handling
* updated model definitions in the vignettes to match manuscript
* add plots representing model fits against observed counts

chicane v0.1.0							2018-08-24
--------------------------------------------------
* First CRAN release

chicane v0.0.3.3						2018-08-09
--------------------------------------------------
* Remove restriction fragments from package
* Slim down extdata folder

chicane v0.0.3.2						2018-06-28
--------------------------------------------------
* Fix fill.in.zeros to replace NAs with zeros across all replicate columns

chicane v0.0.3.1						2018-06-19
--------------------------------------------------
* Add adjustment.terms argument to allow user to adjust for covariates of their choice

chicane v0.0.3.0						2018-06-14
--------------------------------------------------
* Support for parallel processing in cis-interactions model fitting

chicane v0.0.2.10						2018-04-30
--------------------------------------------------
* Expanded test coverage, small code tweaks

chicane v0.0.2.9						2018-04-17
--------------------------------------------------
* Added option for removing counts between adjacent restriction fragments
* Fixed vignette to run without bedtools

chicane v0.0.2.8						2018-04-11
--------------------------------------------------
* Move model fitting try-catch to helper function

chicane v0.0.2.7						2018-04-10
--------------------------------------------------
* Option to store temporary files in specific directory

chicane v0.0.2.6						2018-03-19
--------------------------------------------------
* Added convert.hicup.digest.bed helper function

chicane v0.0.2.5						2018-03-08
--------------------------------------------------
* Vectorize get.id.components function

chicane v0.0.2.4						2018-03-06
--------------------------------------------------
* Bugfix in get.id.components function

chicane v0.0.2.3						2018-03-02
--------------------------------------------------
* Changes to pass CRAN checks 
	- moved gamlss and gamlss.tr to Depends
* Gracefully catch unknown errors

chicane v0.0.2.2						2018-03-01
--------------------------------------------------
* refuse to proceed with data processing if intermediate files already exist
* set data processing examples as \dontrun to get around bedtools dependency on CRAN
* pass keep.files argument through chicane

chicane v0.0.2.1						2018-02-26
--------------------------------------------------
* catch error if model fitting fails after warning


chicane v0.0.2.0						2018-02-15
--------------------------------------------------
* minor test.enrichment bug fix
* catch some --as-cran comments/ warnings
* expanded test coverage


chicane v0.0.1.9						2018-02-14
--------------------------------------------------
* Improvements to test.enrichment:
	- stratified sampling
	- exclude bait-to-bait by default
	- return results as data frame
	- consider proportion of total features 
	- bugfixes

chicane v0.0.1.8 						2018-02-13
--------------------------------------------------
* Revamped data preparation step
* fixed issue where keep.files was not passed through prepare.data


chicane v0.0.1.7						2018-02-12
--------------------------------------------------
* Bare bones enrichment testing


chicane v0.0.1.6						2018-02-05
--------------------------------------------------
* Graceful handling of glm.fitter errors
* Added new level of verbosity


chicane v0.0.1.5						2018-02-02
--------------------------------------------------
* Graceful handling of "no suitable coefficients found" errors
* Pass starting values between distance bins when fitting model 


chicane v0.0.1.4						2018-01-31
--------------------------------------------------
* Retiring some TO DOs
* Minor documentation tweaks


chicane v0.0.1.3						2018-01-30
--------------------------------------------------
* Renamed package
* Added tests for get.trans.count


chicane v0.0.1.2						2018-01-24
--------------------------------------------------
* Error/ warning catching for lack of overdispersion in data
* Added epsilon parameter to be passed to GLM control objects


chicane v0.0.1.1						2018-01-23
--------------------------------------------------
* Switched from VGAM to GAMLSS for truncated distributions
* Added truncated negative binomial
* Added trace and maxit parameters to be passed to GLM/ GAMLSS control objects


chicane v0.0.1.0						2018-01-19
--------------------------------------------------
* Refactored to include run.model.fitting function
* Removed more excess printing


chicane v0.0.0.8						2018-01-19
--------------------------------------------------
* Prettified verbose reports, removed excess printing
* Added smart.split function and incorporated it into split.by.distance

chicane v0.0.0.7						2018-01-18
--------------------------------------------------
* Fixed bug in handling of distance.bins = 1
* Switch to Poisson distribution when negative
  binomial fails to fit


chicane v0.0.0.6						2018-01-17
--------------------------------------------------
* Added truncated negative binomial distribution


chicane v0.0.0.5						2018-01-15
--------------------------------------------------
* Implemented filtering


chicane v0.0.0.4						2018-01-12
--------------------------------------------------
* Option to include zero counts in data (all or cis-only)
* Minor bug fixes and sanity checks


chicane v0.0.0.3						2018-01-09
--------------------------------------------------
* Fixed trans count calculation


chicane v0.0.0.2						2018-01-03
--------------------------------------------------
* Removed other end adjustment from non bait-to-bait model
