Changes in version 3.0.0 (2019-05-09)
 - Code cleanup and refactoring
 - Bug fixes
 - Use readr and stop relying on system commands (grep, sed, gunzip) to read seqz files
 - Use the package pbapply for progress bar
 - Normalize each sample separately
 - Provide coverage profile of the 2 samples separately, before and after normalization
 - Provide CG-content vs depth profile for each samples, before and after normalization
 - Draw standard "mirrored" BAF (from 0 to 1) in the raw genome view


Changes in version 2.1.2 (2015-08-18)
 - Keep the order of the bases corresponding to the major and minor alleles as in the normal sample. (allows mocking haplotype).
 - Fix check for NOTES in newer R versions

Changes in version 2.1.1 (2015-01-20)
 - Fix heterozygous detection when importing VarScan2 data of very high coverage seq.
 - Cleanup sequenza-utils.py
 - Update citation info to published manuscript

Changes in version 2.1.0 (2014-10-08)
 - Add sequenza-utils.py function bam2seqz
 - Add raw data depth-ratio/Bf in the genome view plots
 - Results model fitting plot using the B-allele/depth-ratio plot.
 - Present alternative solutions using local maxima of the CP plot.
 - Model the expected B-allele frequencies with a t-distribution using the observed sd, rather then taking the 95% of the observed Bf.
 - Use dt instead of dbinom for the BAF and depth ratio model.
 - Fix documentation discrepancies on the sequenza-utils.py execution.
 - Add breaks as optional argument - enables to input custom segmentation -
 - Add different segmentation options, fast, het and full, corresponding to different resolutions.
 - Minor fixes.

Changes in version 2.0.0 (2014-04-08)
 - Change seqz names header and some function arguments/formats to improve usability
 - Add to sequenza.fit a method argument to calculate cellularity and ploidy also from mutations
 - Change the recommended file extension from ".abfreq" to ".seqz" for clarity.
 - The "seqz" file now contains a column with strand orientation information.
 - "cp.plot" now plots the scaled log-likelihood.
 - "theoretical.depth.ratio" now implements the correct formula.
 - The "theoretical.*" functions have their arguments rearranged, and defaults changed, for consistency.
 - "sequenza.extract" now has additional filtering arguments.
 - Miscellaneous cleanup/simplification/optimization.

Changes in version 1.0.5 (2014-02-04)
 - Add a python utility for binning the data to a desired window size (reducing vastly memory footprint in the analysis)
 - Fix default workflows parameter to detect CN up to 20.

Changes in version 1.0.4 (2014-01-16)
 - Add function to import VarScan2 output
 - Add results function, to save results and standard plots.
 - Fix error on loading non-zipped files in the workflow.
 - Ignore error and finish the process if one of the chromosome fails in the workflows.

Changes in version 1.0.3 (2013-12-12)
 - Fix grep instructions that broke single chromosome loading
