Alignment residuals in summary do not align with actual feature

[Tarskin]

Summary file lists:

While in reality analytes 762 and 810 were not there.

[Tarskin]

The alignment intermediate file that is created iterates over all features and matches them sequentially to the observed time pairs. The result is that if there is less time pairs than features, the first feature will be coupled to the first time pair that passed alignment criteria.

Specifically, in the listed example the values for 830 were listed as if belonging to 762. The final summary takes its values from the alignment intermediate.

Fix the alignment intermediate files and the summary should be correct again because it matches the feature names to each other.

[Tarskin]

This bug should be solved with b20180405a, and will be closed if no new reports come in.