Alignment and query cleanups #271
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This can be done externally: 1) align -> 2) query. Merging both together makes the interfaces more complex.
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The idea of this change is to keep the alignment separate from search (query).
The query mode will perform operations that return annotation labels with counts for the sequences queried (e.g. via k-mer matching).
The align mode will align to a graph and return alignments with their scores. The reference graph can be a single graph, a subgraph of an annotated graph, or an entire annotated graph. For an annotated graph, this would perform alignment to separate columns and return the alignments (as BLAST).
Any combinations of query and align, such as the current strategy of search with alignment performed against the joint graph followed by querying annotations for the aligned paths, can be done externally in two steps: first run align and pick top alignments and then run query to retrieve the labels for the top alignments.
They don't require the complicated merged interface and can be implemented on the highest level, like Python API.
TODO: implement search(..., align=True) in Python API, as there is no such routine in the core engine anymore.