Changed _count_reported_taxids return type

Renamed variables to clarify their usage and removed gis_container
variable from result because it was unused.
Renamed remove_host_reads

The remove_host_reads is renamed to mark_host_reads to clarify its
usage. Some variables are also renamed. The return type is changed
and now return only the number of host reads. The read_container
is no longer returne as it was passed as an input parameter.
Chnaged determine_host return type

The determine host function doesn't return the read_container any
more because it is passes as an imput parameter. Some varables
are renamed to clarify ther usage.
Remove unused Solver methods

All the methods thata are not used and that didn't have a body
are removed.
Extracted ReadContainer creation from Solver

The ReadContainer is now created and populated outside the Solver.
In this way different kinds of read containers can be supplied to
the Solver. The ReadContainer is now passad to the Solver instead
of the alignment file path.
Add method that returns all read versions

A utility function that returns all reads versions is added. This
will be used to remove the dependency of the RecordContainer to
the ReadContainer.
Extracted RecordContainer creation from Solver

The RecordContainer is now created outside the Solver.
In this way different kinds of read containers can be supplied to
the Solver. The RecordContainer is now passad to the Solver as an
additional parameter.
Removed RecordContaner populate dependency

The RecordContaner was dependent on the ReadContainer for the
population of records. This dependency is now removed by the usage
of a iterable containing nucleotide versions to be loaded.
Fix unit tests for RecordContainer population

The unit tests now use the new popupate method of the
RecordContainer.
Add method that returns existing record

The method fetch_existing_record will return a record only if it is
already loaded into memory.
Remove determine_coding_seqs_optimal dependency

The determine_coding_seqs_optimal was dependent on the
RecordContainer while it only needed a single record from it.