Phase 2

See also outstanding questions.

July 13:

• Add support for multiple indexes and MAF files (done)
• Revisit Enumerator usage (done)
• Chop blocks extending outside a given interval (done)
• Stitch alignment blocks together (done)
• Expose synteny data from 'i' lines better (done)

July 20:

• Convert to bio-alignment representations (basic version)
• Compile list of filter/query features in other implementations
• Search by feature from GFF3/GTF files
• Repackage UCSC bin, 2bit, etc. code

July 27:

• Add CLI tools for Access#find, Access#slice
• Handle negative-strand intervals properly
• Investigate compression formats to support
• Compression work?

August 3:

• Parallelize sequential parsing
• Revisit index overlap optimization
• Explore generalizing the indexing code

August 10: