ASCAT v3.1.3

Update code/doc so it complies with lintr and R CMD check.

ASCAT v3.1.2

1. Improve segmentation for TS (230277f and bc0c905)
2. Output raw (=unmirrored) BAF value for downstream analyses requiring consistent BAF information (62e3da3)
3. Show density in the logR and BAF tracks with darker points (44c0722 and eeb9ccb)
4. Fix a potential issue with R 3.4.0 and the way it handles && (c4c10f8)
5. Update/improve doc (1cca6cc)

ASCAT v3.1.1

Optimisation for ascat.prepareTargetedSeq so it now uses a probabilistic method based on counts to infer genotypes (hom/het/noisy) instead of using fixed VAF thresholds.

ASCAT v3.1.0

Added ascat.prepareTargetedSeq for processing targeted sequencing data.

ASCAT v3.0.0

ASCAT v3 release, including the new ascat.prepareHTS function.

ASCAT v2.5.3

Latest changes before ASCAT v3.0. Changes since v2.5.2: fix for GC% processing, improved plotting functions and some additional platforms.

ASCAT v2.5.2

New version fixes segmentation issue when running multi ASPCF on samples with large number of breakpoints.

ASCAT v2.5.1

created new release

ASCAT v2.5

Added multi-sample segmentation for samples that are expected to share breakpoints.

ASCAT v2.4.4

Merge pull request #10 from Crick-CancerGenomics/dev

Dev