Version 0.8.0 alpha 7

• fix[call]: ref str indexing logic for get_read_snvs

Version 0.8.0 alpha 6

• perf[call]: improve SNV calling performance by reducing disk read (for ref genome) and adding an early escape from a loop
• revert[call]: don't early-return without any read level data

Version 0.8.0 alpha 5

Versus previous alpha:

• perf[call]: performance improvements to SNV component
• chore[call]: improved logging with sample names and more debug logs

Version 0.8.0 alpha 4

• perf[call]: use cached values in more places
• refact[call]: code clean-up for call_locus
• fix[call]: allow non-string JSON keys for debugging purposes

Version 0.8.0 alpha 3

Versus alpha 2:

• chore[call]: improve & make consistent locus-level logging
• fix[call]: handle uncalled useful SNV properly

Version 0.8.0 alpha 2

Versus alpha 1:

• feat[call]: use SNVs to cluster allele peaks for some loci
• feat[call]: include phased SNVs in locus results
• feat[call]: add --snv CLI alias for SNV incorporation
• perf[call]: speed up SNV calling
• chore[call]: type hinting
• docs: update copyright

Version 0.8.0 alpha 1

• BREAKING CHANGE: bump minimum Python version to 3.9
• feat[call]: initial read-level SNV code with --incorporate-snvs CLI flag
• fix[call]: handle None qualities array
• fix[call]: fractional mode crash
• perf[call]: cache segment ref start/end
• perf[call]: move up low-coverage early return to avoid pointless computation
• refact[call]: split caller into multiple files

Version 0.7.2

• feat[viz]: toggle-able Gaussian curves
• fix[call]: properly skip reads with no name
• fix[call]: .item() call error when not in targeted mode
• chore[call]: remove deprecated cigar tuple access
• chore[call]: remove a duplicate variable assignment
• chore[call]: add more type hinting
• chore: update dependencies

Version 0.7.2 alpha 3

• revert something which broke

Version 0.7.2 alpha 2

• fix[call]: .item() call error when not in targeted mode