purple v4.1-rc.1

Functional

• biallelic model changes
• somatic readjustment model in tumor+reference mode
• updated rules for somatic fit and no-tumor classification in tumor-only mode
• restrict somatic variant plotting to target regions only when enabled
• germline chromosomal aberrations support TRISOMY_9P and TERTRASOMY_9P
• SV recovery removed
• disable whole genome dup check for tumor-only non-normal fits
• removed VAF bounds check on hotspots for somatic fitting
• remove indel repeat count from TSG reportability check
• VAF 2% filter for tumor and MSI load
• tumor-only and targeted fits ignore diploid status, no reversion from deleted genes
• VAF threshold 35% to use non-hotspot variant in tumor-only fit
• revert germline adjusted CN change to JCN if not fitted region match found
• fixed germline deletion exon boundaries

Technical

• compatible with Esvee
• removed HRD output from standard run
• calculate target region coding base total using Ensembl instead of CODING tag from BED file
• write empty files on empty/invalid inputs

Bugs

• germline deletion avoid use of next region's min start