Allow references with up to 2**31 contigs

[marcelm]

Note, this is not quite the layout suggested in #421 (comment). I implemented it this way before that comment, but will adjust it.

This changes the RefRandstrobe struct in the following way.

Previous layout:

• 40 bits base hash
• 24 bits auxiliary hash
• 32 bits position
• 23 bits reference/contig index
• 8 bits strobe2 offset
• 1 bit first_strobe_is_main flag

We take 8 bits away from the auxiliary hash and use those bits for the reference
index. New layout:

• 40 bits base hash
• 16 bits auxiliary hash
• 8 bits strobe2 offset
• 32 bits position
• 31 bits reference/contig index
• 1 bit first_strobe_is_main flag

Closes #421

[ksahlin]

great! Let's have a meeting at some point. I want to understand and learn from you some of the design choices in this commit. Like changing hash to a method.

@luispedro had a local version where he moved the offset bits into positions integer. Just tagging him here so that he can see we are now actively working on it with a different layout related to multi-context seeds. An idea we had for a while that we make public soon.

[marcelm]

Happy to talk about this further. To elaborate already now: Making all attributes private improves encapsulation. By forcing any access to the hash value to go through the hash() getter method, the RefRandstrobe class is in full control of how it wants to internally represent hash values. There’s only one place we need to modify if we want to change that representation. In this particular case: I now don’t have to write randstrobe.hash & RANDSTROBE_HASH_MASK everywhere a hash value is used, I can just write randstrobe.hash() and let the method deal with.

Also, as a consequence of making all attributes private and not exposing any methods that allow changing them, RefRandstrobe instances are now immutable. And immutable objects are nice because they make it easier to reason about the state of the program.