v0.3.1

• Add output prefix option (takes directory or directory + prefix name)
• Deprecate outdir (maintain backwards compatibility until v1.0)
• Fix bug in call-reads where a read with partial exon2 (only) coverage blows up candidate pool
• Catch error from aligned inputs with wrong reference

v0.3.0

• NEW call-reads tool for calling Class I alleles directly from aligned HiFi reads (no assembly)
• Extended reports for call-reads data
• Update IPD-IMGT/HLA to version 3.55 (2024-01)
• Add option to limit calls to genomic (full-length) records

v0.2.3

• Option to require exon2 in query
• Improved error handling
• Assembly alignment recommendation (readme)

v0.2.2

• IMGT update to v3.54 (2023-10)
• relax assembly input args (allow single fasta)
• improved error handling

v0.2.0

First release of HiFiHLA.

• IPD-IMGT/HLA Version: 3.53 (July 7, 2023)