pb-StarPhase v0.14.0

Changes

• HLA allele labeling has been updated to improve 4th-field accuracy: When two potential definitions are compared, we now restrict the initial comparison to only the shared regions of the two haplotype sequence definitions (this is often different, especially for DNA sequences). In the event of a tie, we revert to the full-length allele definitions.
• The HLA database configuration has been updated to include strand information for HLA genes. Defaults for HLA-A and HLA-B are set, so no database update is required. This modification will show in the next database release.
• HLA debug consensus outputs will now be output on the strand the gene is located to improve matching to IMGT/HLA sequences. For example, HLA-A is already on the forward strand so no change will be made. In contrast, HLA-B is on the reverse strand so the consensus sequences will be reverse complemented in the output FASTA file.
• Breaking change: CYP2D6 and the HLA genes now share a single debug BAM file through the --output-debug option: debug_consensus.bam
  • The previous debug file for CYP2D6, cyp2d6_consensus.bam, has been removed from the outputs. The mappings from this file have been moved into the new debug_consensus.bam file.
  • For both HLA genes, the BAM file contains alignments of the HLA consensus sequences and corresponding read sequences used to generate the consensus. Additionally, if the assigned haplotypes have DNA sequences in the database, those sequences are also aligned for comparison purposes.
  • Previously deprecated option --debug-hla-target has been repurposed to allow for specification of additional HLA haplotypes to get mapped in this debug BAM. As with the assigned haplotypes, these must have a DNA sequence in the database to get mapped.