make compact ulong store dynamic about genometools

[satta]

It would also be a good idea to compare the GtCompactUlongStore with the other byte-compressed array classes in core/ (BitPackArray/BitPackString/...) in terms of functionality and efficiency and maybe consolidate them such that only one `good'' implementation remains. These classes in core/ are not really widely used ayway IIRC.

[Garonenur]

just for future reference:

• core/bitpackarray.h
  • is a simplyfied interface to core/bitpackstring.h
  • static, # of elements has to be known
• core/bitpackstring.h
  • from Thomas,
  • some automatic generated code
    • seperate code for different uint_X types
  • many inline functions
  • some code duplication,
  • not a class
  • complicated code.
• core/compact_ulong_store.h
  • from Stefan
  • very simple interface
  • static, # of elements has to be known

[gordon]

If it would be possible to remove the bitpackstring code that would be great. The automatically generated code is very hard to maintain.

[satta]

We should figure out whether one of these actually subsumes one (or all?) of the others. We definitely should remove this redundancy and stick with one GOOD implementation (and prefereably not the autogenerated one).

[satta]

If I run git grep bitpackstring.h it turns out that the bitpackstring stuff is only used in the simplified bitpackarray interface (which is used in Readjoiner and the Encseq implementation) and the match/eis-* packed index code. I only know how the Encseq code uses this functionality, and it is simply sequential writing and random access to a compressed 32-bit integer array of a given length. I guess that could be done with the GtCompactUlongStore as well, as long as it is (made?) Mapspec-compatible.
I don't know about the other use cases, especially Readjoiner and the packed index stuff.

[ggonnella]

I checked the places in Readjoiner where bitpackarray.h is used. The operation needed there are new/delete, get/set a value, get total size of the representation (for writing to file); these are all operations also available with compact_ulong_store.h. Therefore, as far as I am concerned, GtBitpack can be deleted.