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/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/63DMS compatibility between OSX and Ubuntu (Linux?)2019-09-25T12:57:46ZCeline MercierDMS compatibility between OSX and Ubuntu (Linux?)There is an error when reading a DMS imported from an OSX system on Ubuntu. Needs further testing.There is an error when reading a DMS imported from an OSX system on Ubuntu. Needs further testing.Celine MercierCeline Mercierhttps://git.metabarcoding.org/obitools/obitools3/-/issues/59Basic R API2020-05-30T14:59:11ZCeline MercierBasic R APIBuild a basic R API to at least fill a R dataframe and a metabaRffe object with a viewBuild a basic R API to at least fill a R dataframe and a metabaRffe object with a viewCeline MercierCeline Mercier