Re-working FMDIndex to hopefully work with the new schema.
Hacked up other Avro to not break the build
Some attempted patches to get build working again
Removed all the old sequence graph stuff, leaving just the reference graph stuff. Now builds to the point where I can run tests, and promptly segfaults.
Can test without segfaulting and some basic tests pass
Fixing basig position conversion functions
All FMDIndexTests pass
Adding a MergedReferenceStructure that *ought* to be able to read createIndex indices
Fixing up createIndex argument parsing, and redirecting its .sh
Running createIndex as part of tests
Some hierarchy tests pass, some fail. Also added test utility file I forgot.
Added a bunch of BWT debugging dump methods
Also tests that use them.
Re-aligned ranges and Sides
Dumping mappings