Changes in version 1.9.3 (2021-01-28)
-------------------------------------

o Now defaulting to exclude sex chromosomes from model fitting
o Also included sgc argument in twosamplecompare
o Data frame output of ACEcall and twosamplecompare are now restricted to selected chromosomes


Changes in version 1.9.1 (2021-01-15)
-------------------------------------

o accommodating fitting of chromosomes with only a single germline copy (e.g. X and Y in males)
o added the option to specify which cellularities to include in squaremodel
o option to save readCounts-object in runACE


Changes in version 1.5.2 (2020-04-14)
-------------------------------------

o updated maintainer e-mail address


Changes in version 1.5.1 (2020-01-14)
-------------------------------------

o fixed a bug in getadjustedsegments that joined adjacent chromosomes with same segment values


Changes in version 1.1.2 (2019-04-23)
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o added citation information!
o fixed bug in getadjustedsegments and twosamplecompare with non-matching NAs


Changes in version 1.1.1 (2018-11-13)
-------------------------------------

o added forcesegmentsontemplate function
o speed boost by small coding change in model fitting
o added argument in loopsquaremodel to make returning the models optional and flexible (see documentation)


Changes in version 0.99.6 (2018-07-26)
-------------------------------------

o bugfix in linkvariants: no default freqindex


Changes in version 0.99.4 (2018-06-26)
-------------------------------------

IMPROVEMENTS

    o changed linkmutationdata to linkvariants
	o linkvariants can estimate copies of heterozygous germline variants
	o linkvariants calculates the upper and lower bound of a given confidence level when read depth is given
	o changed postanalysisloop to accommodate linkvariants
	o added argument in runACE to specify genome build
	o several minor documentation amendments
	o improved coding robustness using seq and seq_along functions


Changes in version 0.99.0 (2018-05-24)
-------------------------------------

SUBMISSION

    o initial submission to Bioconductor
