Detect I/L and N/D

[douweschulte]

In GitLab by @nonnominandus on Feb 10, 2021, 19:04

If there is a known Isoleucine in the input data it can be assumed that all Leucines matched on that position are actually Isoleucines. But one of the problems is that Peaks does not assign Isoleucines (even though sometimes they could be known in theory) so added this would not immediatly fix al I/L problems. THere should be some thought gone into handling the I/L assignment based on the template as well to try and get the correct amino acid.

The same is broadly speaking true for N/D.

[douweschulte]

In GitLab by @nonnominandus on Mar 25, 2021, 10:50

If needed it is possible to loop over all input data and use the available 'rules' to determine I/L within this program. This would remove the need to be dependent on the previous program to do these analyses.

By Douwe Schulte on 2021-03-25T09:50:13 (imported from GitLab)

[douweschulte]

In GitLab by @nonnominandus on Jun 1, 2021, 17:05

As Peaks does not do any analysis of I/L (just reports L) any function like the above will inevitably fail. On a later moment it would be cool and helpful if the analysis could be done, but that likely requires access to raw files.
[DiscussionPoint] For the time being it could be beneficial to force the I/L configuration of the germline sequence independent of the input reads (or give the option to do this with a parameter).

By Douwe Schulte on 2021-06-01T15:05:50 (imported from GitLab)

[douweschulte]

In GitLab by @nonnominandus on Jun 3, 2021, 14:40

Forcing germline I/L can be implemented

By Douwe Schulte on 2021-06-03T12:40:03 (imported from GitLab)

[douweschulte]

In GitLab by @nonnominandus on Jun 18, 2021, 16:52

mentioned in commit c9965857b3f9c97b69c23a587b395a03fff1e41d

By Douwe Schulte on 2021-06-18T14:52:27 (imported from GitLab)

[douweschulte]

Any further work will be implemented based on ideas like #197. So this issue can be closed.