Use reference-specific primer coordinates #72
Merged
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This replaces the single (giant) forward and reverse set of primer coordinates (
FWList
&RVList
) that was used previously. Now two dictionaries are used (forward and reverse), keyed by ReferenceID and containing a set of primer-coordinates as value.The correct set of primer-coordinates is then used by looking up which ReferenceID a read maps to and only using the corresponding primer coordinate set from that reference in the downstream read-cutting process