Battenberg v2.2.10

Please note:
Users are recommended to keep using v2.2.9 until v3 of Battenberg is ready. This is an interim release for the convenience of our friends at the Sanger Institute, incorporating changes that are required for their pipeline system.

Battenberg v2.2.9

• Rewrite of GC correction code
• Inclusion of replication timing correction
• Inclusion of SV breakpoints made easier
• Increased decimal precision
• Various bug fixes
• Extended README

Battenberg v2.2.8

• Fixed synchronisation of alleles at start of the pipeline
• Fixed quirky behaviour of sv_breakpoints_file in callSubclones
• Fixed calculation of rho when calculating solution based on reference segment
• Fixed mismatch when data with "chr" in chromosome names was provided
• Fixed case where the number of SNPs with logR wasn't checked, sometimes leading to errors
• Added Dockerfile
• Integrated pipeline into the R package (battenberg function)

Battenberg v2.2.7

• Speed improvements to impute2
• SNP6 pipeline now takes into account homozygous SNPs
• various new figures added
• various smaller convenience functions
• documentation cleanup

Battenberg v2.2.6

• logR is now also tested during merging
• No longer masking negative copy number segments at initial fit
• Reverted parsing of BAFsegmented back to native read.table as readr was causing issues for some cell line data with alterations at the start of chr1

Battenberg v2.2.5

• Added option to select how BAF per segment is calculated (median or mean)
• Fixed bug in nonrounded figures where alleles were switched

Battenberg v2.2.4

Various small changes improving speed, adding small functionality and fixing a couple of small issues.

Battenberg v2.2.3

• Adding read_table_generic function that speeds up reading in data
• Various small fixes

Battenberg v2.2.2

• Fix issues with merging segments and ploidy calculation for figures
• Added recalculation of GC content correlations after correction

Battenberg v2.2.1

• Mask high copy number segments
• Fixes to purity/ploidy boundaries
• Cleanup
• Various smaller bugfixes