purple v4.4

Functional:

• adjusted targeted TML calc
• TMB and TML raise min VAF of 0.02 -> 0.05
• targeted panels use chrX region size to determine Amber gender
• clustering only uses Amber BAF PCFs if follows another one and not at start or end of an arm
• restrict fitting hotspots to 5% VAF
• cosmetic changes to circos plot
• show driver genes on Circos plot
• use Redux MSI prediction file for panels, removed support for MSI sites file config and logic
• aneuploidy detection to impact somatic fit
• removed deleted genes logic for panels
• call germline AMPs as well as DELs
• segment around excluded IG regions
• find driver for LOH events with zero likelihood
• find drivers splice region without gene impact and zero likelihood
• added LIKELY_DIPLOID GermlineStatus for diploid percentage 0.7-0.85 and 1.15-1.3

Bugs:

• fixed driver multi-hit routine impacting biallelic status
• check depth window count and SV-bounds for germline amp-dels
• tumor-only mode use BAF fit if highly diploid and high purity if BAF within specified limits
• fixed indel colours in main Circos plot
• fix plot fail when unable to determine maxPloidy. Replace deprecated ggplot 'size' arg with 'linewidth'
• remove duplicate COHORT_AMP_DEL_FREQ_FILE constant
• segments created for excluded regions to have start segment support EXCL

Technical:

• when splitting segments by excluded regions, assign the new segment support type "EXCL" to new fragments
• dropped chimerism field from QC, fixed 2-hit DNDS logic from non-impacting variants
• removed targeted panel ratio file, replaced by optional config: target_tmb_ratio, target_tml_ratio, target_coding_factor
• in finding structural variants that match amplified regions, use orientation -1 at the start and 1 at the end
• handle cohort germline amp-del file if not sorted

Config:

• germline_del_freq_file -> germline_amp_del_freq_file
• optionally filter SVs with config: sv_qual_filter
• add redux_tumor_dir - to load MS production file for panels