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ecotag: added separate threshold for minimum circle identity (and switch

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to version 3.0.0b35
This commit is contained in:
Celine Mercier
2020-09-25 16:22:09 +02:00
parent 11a0945a9b
commit c4696ac865
5 changed files with 36 additions and 14 deletions
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7
src/obi_ecotag.h
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@ -42,12 +42,14 @@
* @param output_view_name The name to give to the output view.
* @param output_view_comments The comments to associate to the output view.
* @param ecotag_threshold The threshold at which to assign.
* @param bubble_threshold The threshold at which to look for an LCA (i.e. minimum identity considered for the assignment circle);
* the threshold actually used will be the highest between this value and the best assignment score found.
*
* The algorithm works like this:
* For each query sequence:
* Align with reference database
* Keep the indices of all the best matches
* For each kept index, get the LCA at that threshold as stored in the reference database, then the LCA of those LCAs
* For each kept index, get the LCA at the highest threshold between bubble_threshold and the best assignment score found (as stored in the reference database), then the LCA of those LCAs
* Write result (max score, threshold, taxid and scientific name of the LCA assigned, list of the ids of the best matches)
*
* @returns A value indicating the success of the operation.
@ -65,7 +67,8 @@ int obi_ecotag(const char* dms_name,
const char* taxonomy_name,
const char* output_view_name,
const char* output_view_comments,
double ecotag_threshold);
double ecotag_threshold,
double bubble_threshold);
#endif /* OBI_ECOTAG_H_ */