export of pruned lineages doesn't indicate pruning

[julou]

Hello,

We are trying to make a more extensive use of pruning to detect some cell lysis events…
Doing so, I realised that the end_type variable of a pruned lineage is set by what happens downstream of pruning (one of exit / div / eod). I think that the general behaviour should be to set the end_type to "pruned".

Thanks!

[julou]

this has stronger implications that I initially thought:
in most analysis with this type of data (including previous papers by other labs not using MoMA), one focuses on cells that have been tracked from birth to division (mostly to discard cells that exit before dividing). The easy way to do this is to filter cells not born at time 0 and with end_type == 'div'.

Due to this bug, the second criteria is not matched since a cells that is pruned an divide between the pruning point and its exit will be marked as end_type == 'div' although it's not tracked until division…

So it is important fix not to mislead users in their downstream analysis.