Reduce output RAM usage / Change the way << operator works

edawson / gfakluge

A C++ library and utilities for manipulating the Graphical Fragment Assembly format.

http://edawson.github.io/gfakluge/

MIT License

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Reduce output RAM usage / Change the way << operator works #28

Open edawson opened 6 years ago

edawson commented 6 years ago

String output currently builds a stringstream, which is fine for small graphs but pretty ugly for huge ones. We should refactor this. One suggestion:

Have a helper function that takes an ostream (either fstream or stringstream).

to_string calls this, passes a stringstream, and returns that stringstreams .str() call.
<< calls this and passes a generic ostream.

edawson commented 6 years ago

Another thought - we should refactor away from the OG GFA1 structs. We can just represent everything under the hood in GFA2 structs. This prevents the madness that is the gfa_1_ize() and gfa_2_ize() functions.