NEWS

Changes in version 1.25.1
+ Bugfixes:
- fixed issue with R4.3 ("cannot xtfrm data frames")
- fixed documentation
- updated description file

Changes in version 1.21.2
- increased upper bound for enrichment model, allowing for a steeper increase in enrichment with CpG density. (Github PR \#9)


Changes in version 1.21.1
+ Bugfixes:
- makeTable with one window (github PR \#8)

Changes in version 1.7.4
+ Reformated NEWS file

Changes in version 1.7.3
+ Adapted vignette to BiocManager installation process

Changes in version 1.7.2
+ Bugfixes: 
- addCoverage fixed fragment size sd for chromosomes with 1 read
- addCoverage fixed missing regions in count_matrix for chromosomes without any reads

Changes in version 1.7.1
+ Bugfix: addCoverage crashes when there are no reads for chromosome/contig

Changes in version 1.5.1
+ Bugfix: Crash due to changes in getOverlaps

Changes in version 1.3.2
+ New feature:
- select active BSgenome masks for pattern density estimation
+ Bugfix:
- adaptions to changed behavior of GenomicRanges

Changes in version 1.3.1
+ transition to Github

Changes in version 1.1.6
+ New Feature:
- addNewSample function

Changes in version 1.1.5
+ New Feature:
- multicore support for GLM fitting

Changes in version 1.1.4
+ Bugfixes:
- fitting of GLM crashed when applied genome wide on > 150 samples

Changes in version 1.1.3
+ Updated citation.
+ Runtime improvement:
- direct implementation of quantile function 
    using quantile function of gamma distribution

Changes in version 1.1.2
+ Bugfixes:
- addCNV: Fixed crash when only one normal sample is present
- addCoverage: fixed chr sorting issue in absence of bam index

Changes in version 1.0.0
+ first stable release

Changes in version 0.99.6
+ Bugfixes:
- addCNV: check for sample table now checks specified files for CNV

Changes in version 0.99.5
+ New features
- user level functions now have sample id check
- more detailed tutorial, including case study
+ Bugfixes:
- makeTable: fixed groupMeans without individual samples

Changes in version 0.99.4
+ New functions:
- multicore support for bam file processing
- memory and runtime optimizations
+ Bugfixes:
- bug in consideration of zygosity of chromosomes

Changes in version 0.99.3
+ Bugfixes:
- updated imported NAMESPACE 

Changes in version 0.99.2
+ New functions:
- option to set ploidity for chromosomes, i.e. to account for sex chromosomes
+ Bugfixes:
- fixed bug resulting in NA values at quantile calculation for beta estimates
- minor fixes
+ Documentation:
- changed vignette builder to knitr/BiocStyle/html


Changes in version 0.99.1
+ Bugfixes:
- fixed crashing plotCoverage with one sample
- qseaPCA-show
- typo in error-message of getOffset (rpw)
- resolved namespace issues

Changes in version 0.99.0
+ Submission to Bioconductor