v1.1.17:
- Remove Additional_repositories from DESCRIPTION.

v1.1.16:
- Set min_overlap = 0L in bed_intersect() calls for valr 0.10.0 compatibility

v1.1.15:
- Replace row-wise apply() overlap counting in .wmeanvec() with vectorized overlap-length computation.
- Vectorize transcript-to-window splitting in makewindows() internals (remove cluster-based parallel approach).
- Reduce repeated maptrack reads by optionally loading the full track once and filtering per chromosome.
- Improve .retrievebgval skipping conversion to data.frame.
- Update docs/version/NEWS accordingly.

v1.1.14:
- Fix: Add missing expdf argument to plotmulti internal functions.

v1.1.13:
- Remove unused variable in genesECDF.
- Remove digit in variables.
- Fix bug due to row and col names in teprmulti.
- Add table of contents to vignette.
- Add installation section to vignette with GitHub install instructions.
- Standardize all stop() error messages with consistent '[tepr] Error:' prefix.
- Standardize all warning() messages with consistent '[tepr] Warning:' prefix.
- Fix incorrect warning text in plothistoknee and plotmetagenes (previously
  said 'auc' when displaying histograms and metagenes).
- Refactor the error messages in the tests for consistency and clarity.
- Replace deprecated 'size' with 'linewidth' in geom_line (ggplot2 3.4.0+).

v1.1.12:
- An error message is now appearing if the user provide a wrong experiment table.
- Change the test formula for the direction and strand columns in the checkexptab function that was triggered unexpectedly when an incorrect exptab was provided.
- Add a testthat for the checkexptab function.

v1.1.11:
- Add indications in the error message of meandifference function if the user has more than two conditions.
- In the vignette, the chromosomes are now imported from the package instead of downloading them from the web.

v1.1.10:
- Export function from MASS to match ggplot2 update.
- Replace SeqinfoForUCSCGenome by retrievechrom in vignette to avoid online resources problems.

v1.1.9:
- Unhide and export .retrievechrom function and use it to create chromtabtest in tests to avoid error due to online ressource problems.
- Update documentation.

v1.1.8:
- Remove acronym in package title.
- Remove listing of technology acronyms in Description of DESCRIPTION.
- In documentation, replace dontrun by donttest if the example cannot be run or takes more than 5 seconds.
- Use tempdir() instead of getwd() by default.
- Change package title from "Transcription Elongation Profile" to "Transcription Elongation Profiling". Acronym "tepr" is kept.
- Remove the joinfiles function that was used during the bash processing.
- kneeallconds can now be run independently of the number of conditions.
- \dontrun is used in the examples of functions handling more than two conditions: plotmulti and teprmulti.
- package is now available on CRAN.


v1.1.7:
- Replace all identical tests by equal in testthat.
- Remove the use of BiocStyle for the vignette.
- Move pictures to inst/extdata.
- Replace markdown image integration with knitr.
- Add check on the type of chromtab at beginning of preprocessing function.
- Remove all uppercase in package name in all files.
- Remove redundant 'in R' when mentionning package name.
- Version submited to CRAN waiting for approval.


v1.1.6:
- Create release to obtain doi on Zenodo.


v1.1.5:
- Update URL to black list repository.
- In vignette, add missing url to cugusi.tsv.


v1.1.3:
- In the subfunction .divideannoinwindows of makewindows, replace hardcoded 200 by nbwindows.
- Add filter chromtab in quickstart of the vignette.
- In vignette, limit chromtabtest to chr13.
- Add verifications on chromosome names in preprocessing and blacklisthighmap functions.
- Add forcechrom param to the preprocessing and blacklisthighmap functions and modify documentation.
- In preprocessing.R, add forcechrom = TRUE in .createbedgraphlistwmean because the verification is done at the start of the preprocessing function.
- Set showtime default to FALSE in createtablescores.
- Add test on genome name and chromtab at beginning of preprocessing.
- Set genomename to NA and saveobjectpath to getwd() by default in preprocessing function.
- Add countna to the error message of .extractstr in utils.R.
- Add information to the error messages in .extractstr (utils.R), .condcolidx (meandifference.R), averageandfilterexprs and .expressedtrans subfunction, createtablescores, .checkempty (allauc.R), .computeupdown (attenuation.R).
- Add tests in the tests/testthat folder for each function.
- Add zenodo download commands in the vignette. Data are under doi 10.5281/zenodo.15050723.
- Add code to avoid triggering warnings in blacklisthighmap, .removeblackandlowmap, .retrievemaptrack.
- Remove tidyselect deprecated message in universegroup.R (lines 119, 127, 143, 153).
- Add in testthat condition for macos: Evaluate equality instead of identity.
- Add doi after merging with main branch.
- Modifications upon suggestions by "R CMD check --as-cran": Set title in case and remove the first sentence of description in DESCRIPTION, change black list url in vignette.


v1.1.2:
- Modifications and corrections to pass R CMD check.
- Creation of .returnexpcolnames in utils.R.
- Simplification of averageandfilterexprs and create subfunction .expressedtrans.
- In .computeecdf, under the comment "Shrink the results back to the transtable keeping ecdf columns", change code to remove the 'dot' usage which throws an error by R CMD check.
- In .computeecdf, also change the way column names are modified under the comment "Removing strand from column names" for the same reason.
- In .normalizeandsummarize, replace code for "Selecting coord and mean values" to remove the use of dot.
- Add a .github/workflows that test the package on windows, macos, and ubuntu
- Add a .Rbuildignore to exclude the .github folder and manual.pdf during package creation
- Correct bug about direction in loop if dfstrandlist of the function .expressedtrans in averageandfilterexprs.
- Folder inst/extdata reduced from 111 Mb to 504K
- Add error if no transcript is identified as expressed in averageandfilterexprs. This case prevents the rest of the  code to be executed.
- Add a README.md
- Change outfold = "." parameter to outfold = getwd() in plotauc, plotecdf, plothistoknee, plotmetagenes, and plotmulti to avoid potential errors with windows.
- Change tmpfold = "./tmp" to tmpfold = "tmp" in blacklisthighmap and preprocessing to avoid potential errors with windows.
- Change finaltabpath = "./" to finaltabpath = getwd() in createtablescores and preprocessing to avoid potential errors with windows.
- Change workingdir = "." to workingdir = getwd() in joinfiles.
- Rename the default 'tmp' folder by 'tmptepr' to avoid issues of pre-allocated space. Define the default path with file.path(getwd(), "tmptepr").
- In .mergefiles of createtablescores, add specific code when OS is windows. It uses a power-shell syntax and system2.
- add file encoding utf8 for windows check in createtablescores.

-- vignette
- With the reduced data of the package, the preprocesssing in the "quick start" section of the vignette now takes 38 seconds instead of 7 minutes.
- Use two different exptab in the package. One for preprocessing and one for the downstream analysis. The code of the quick start section is modified accordingly.
- The downstream part is now done on 6 transcripts instead of a 100. This aims at reducing the size of the package.
- Display the results of the quick start code
- Improve preprocessing description
- Reduce code in different sections since quickstart is now executed in background
- Add '?' before function names
- add figure of the global structure of the package
- remove explicit path to current directory and use getwd where appropriate
- remove outfold from plot functions in annex
- add optional line in quickstart to get chromtab
- remove preprocessing in bash section


v1.1.1:
- Optimize the vignette text with Gemini.
- Update output of the full tepr analysis in annex of the vignette.
- Add allauc and update doc of kneeallconds.
- Updated pictures in vignette.


v1.1.0:
- Create a showallcomp function to choose what to exclude in teprmulti dontcompare parameter.
- Create a kneeallconds function that enables to calculate knees for each condition separately.
- Create section 5.4 "More than two conditions" in the vignette with the "teprmulti analysis", "plotmulti", and "Calculating knee for each condition" subsections.


v1.0.4:
- Remove dontcompare parameter from allauc and tepr.
- Add code to remove conditions with a dontcompare vector in teprmulti.


v1.0.3:
- tepr can now handle a single condition. See section 5.6 of the vignette.


v1.0.2:
- Add functions teprmulti and plotmulti to use when more than two conditions are present. New sections 5.4 and 5.5 of the vignette.


v1.0.1:
- Solve bug due to chromtab parameter.
- Chromtab is now a parameter in case of connection hickups.
- Manual has been updated.
- Add code to vignette to use the data provided with the package.


v1.0.0:
- Preprocessing is now done in R.


v0.0.99:
- Pre-processing with bash.
