`--order_by_timepoint` not working

[abenjak]

Hello,

--order_by_timepoint option is not implemented yet, but this is not documented. Therefore the order of samples in the SIF file MUST be ordered by timepoint, otherwise all the results (except for the pie charts) will be assigned to wrong samples, i.e. samples will be swapped.

For example, this SIF file is correct:

sample_id  maf_fn            seg_fn  purity  timepoint
3X_T       3X_T_ABS_MAF.txt          0.22    1
3X_M       3X_M_ABS_MAF.txt          0.26    2

But this will produce wrong results:

sample_id  maf_fn            seg_fn  purity  timepoint
3X_M       3X_M_ABS_MAF.txt          0.26    2
3X_T       3X_T_ABS_MAF.txt          0.22    1

Best, Andrej