pb-StarPhase v0.13.1

Changes

• For HLA genes, StarPhase would previously ignore any HLA allele definitions that were missing a DNA sequence in the database. StarPhase now allows these partial HLA allele definitions by default.
• A new option was added to enable the previous behavior: --hla-require-dna. If this option is enabled, any HLA allele definition that is missing a DNA sequence will be ignored and never reported in StarPhase outputs.

Fixed

• Fixed an issue where a CYP2D6 deletion allele (*5) could be reported on the same haplotype as another allele. While this is biologically possible (e.g., deletion of one *10 in a "*10x2" haplotype), it is not considered a valid star-allele at this time. This combination will still show up in the debug log files, but it will get filtered in final reporting. For example: a "*10+*5" haplotype will now get reported as "*10".