Questions

Outstanding questions about MAF and MAF workflows:

• Is it useful to build indexes on other sequences besides the reference sequence?
• Should the score field of an alignment block be zeroed or removed whenever the block is modified?
• How, precisely, should selection based on features in GTF/GFF3 files work?
• When converting a MAF Block/Sequence to bio-alignment representation, how should we handle quality metadata (from 'q' lines), which is tied to the actual sequence data and would need to be maintained in parallel if a column were deleted?
• Is supporting the bx-python index format still desirable? Performance with Kyoto Cabinet indexes seems competitive, and the indexes are neither very large nor very expensive to build.
• Blankenberg et al. mention this filtering mode: "removing blocks which have aligned species occurring between non-syntenic chromosomes or strands" which is unfortunately a bit cryptic.
• Are coverage statistics useful or appropriate to provide?