examples: fix compiler warning about unused variable

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
transport: use red-black tree instead of binary heap

The current implementation of the binary heap uses an array.
Inserting into the heap can be O(n) when the array is full and
needs to be resized.

Until the binary heap is implemented with pointers, the multiplexer
is going to rely on the red-black tree.

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
scheduler: use red-black tree for scheduling actors

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
structures: add an abstraction layer for binary heap

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
examples: fix trailing spaces

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
unitig_visitor: don't count the same graph store twice

When a graph store has nothing more to produce, but other graph
stores still do, a graph store may be counted more than once.

This change fixes this bug.

Suggested-by: Élénie Godzaridis <telomerika@gmail.com>
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
genomics: use Doxygen comment for structure

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
graph_store: add some assertions for the iterator

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
unitig_walker: fix a bug in completion verification

A walker may count a given graph store more than once.

To avoid that problem, reset the counter when the index
is rewinded back to 0.

This solution was suggested by Élénie Godzaridis.

Suggested-by: Élénie Godzaridis <telomerika@gmail.com>
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: add action ACTION_ENABLE_VERBOSE_MODE

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
unitig_visitor: add support for ACTION_ENABLE_VERBOSE_MODE

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
unitigs: reduce verbosity in the visitor code

Link: https://github.com/GeneAssembly/biosal/issues/799
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium_actor: add lightweight counters for actor messages

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
biosal_unitig_visitor: use local velocity instead of global velocity

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
visitor: add inbound and outbound throughputs

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: move the code that prints runtime information in a function

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium_node: track last received message and sent message counts

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: polish the debugging information reported by thorium

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: rename -print-load to -print-thorium-data

This option prints more than just load information.

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium_node: write log file at the end to avoid discarding information

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>