OBITools3 issueshttps://git.metabarcoding.org/obitools/obitools3/-/issues2022-04-20T05:32:26Zhttps://git.metabarcoding.org/obitools/obitools3/-/issues/122build_ref_db: taxonomy needs to be in the same DMS as the ref sequences but i...2022-04-20T05:32:26ZCeline Mercierbuild_ref_db: taxonomy needs to be in the same DMS as the ref sequences but it shouldn't be the caseWhen running the build_ref_db command, the taxonomy is not read if it is not in the same DMS as the reference sequences. It was a choice at the time, but it feels more annoying now. (At least proper error handling should be implemented)When running the build_ref_db command, the taxonomy is not read if it is not in the same DMS as the reference sequences. It was a choice at the time, but it feels more annoying now. (At least proper error handling should be implemented)Celine MercierCeline Mercierhttps://git.metabarcoding.org/obitools/obitools3/-/issues/113obi rename2021-07-21T03:29:14ZEric Coissacobi renameI have a prankster keyboard that likes to duplicate characters. So I regularly make typos. When using `obi ngsfilter` I used the `-u foo/uunidentified` option instead of `-u foo/unidentified`. I would like to rename the `foo/uunidentified` table to `foo/unidentified`. I can't find a solution. Can we expect a `obi rename` or `obi mv` that will do this?
Thanks ;-)I have a prankster keyboard that likes to duplicate characters. So I regularly make typos. When using `obi ngsfilter` I used the `-u foo/uunidentified` option instead of `-u foo/unidentified`. I would like to rename the `foo/uunidentified` table to `foo/unidentified`. I can't find a solution. Can we expect a `obi rename` or `obi mv` that will do this?
Thanks ;-)https://git.metabarcoding.org/obitools/obitools3/-/issues/99ngsfilter: identify primer dimers2021-03-21T20:53:15ZCeline Mercierngsfilter: identify primer dimers`ngsfilter` currently tags primer dimers with the 'reverse primer not found' error. Ideally it should detect the reverse primer overlapping on the forward primer, and there would be a 'primer dimer' error. This is not the case at present because the forward primer is cut out of the sequence once it is found.`ngsfilter` currently tags primer dimers with the 'reverse primer not found' error. Ideally it should detect the reverse primer overlapping on the forward primer, and there would be a 'primer dimer' error. This is not the case at present because the forward primer is cut out of the sequence once it is found.https://git.metabarcoding.org/obitools/obitools3/-/issues/79Dictionary efficiency issue2020-04-23T14:02:58ZCeline MercierDictionary efficiency issueHandling of huge dictionaries (typically merged information like merged taxids in reference databases with hundreds of thousands of taxids or merged samples in datasets with thousands of samples) is not efficient as it creates big files that are not mapping-friendly (and occupy a lot of disk space).
There is already a solution half implemented in the form of dictionaries stored as characters strings, but the API to parse them in C is not implemented, so it's not or rarely used. This would be the fastest solution to finish to implement, but eventually a better solution could be developed (e.g. using hash tables implemented in a way that makes the most of the mapping behaviour).Handling of huge dictionaries (typically merged information like merged taxids in reference databases with hundreds of thousands of taxids or merged samples in datasets with thousands of samples) is not efficient as it creates big files that are not mapping-friendly (and occupy a lot of disk space).
There is already a solution half implemented in the form of dictionaries stored as characters strings, but the API to parse them in C is not implemented, so it's not or rarely used. This would be the fastest solution to finish to implement, but eventually a better solution could be developed (e.g. using hash tables implemented in a way that makes the most of the mapping behaviour).Celine MercierCeline Mercierhttps://git.metabarcoding.org/obitools/obitools3/-/issues/62Multithreading2019-07-24T11:58:28ZCeline MercierMultithreadingImplement OpenMP parallelization (and maybe others) wherever possible (first obvious candidate: obi align).Implement OpenMP parallelization (and maybe others) wherever possible (first obvious candidate: obi align).Celine MercierCeline Mercier