Fix a bug in the Jaqaman linker preveting it from returning ALL assignments.

A bug introduced by trying to write a sparser version of the linker,
which is probably useless on top of that.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Remove useless settings in the settings map.

The CUTOFF percentile is not userd (not even by Nick LAP tracker, which
is weird). The BLOCKING_COST as well, since we have a sparse matrix now.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Fix a bug in SparseCostMatrix transpose method.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
Add a method to SparseCostMatrix to write a value to all non-sparse values.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
WIP: work on the gap-closing only case.

Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>