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Update updates.md
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lauraluebbert committed Jan 22, 2024
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- Changed ortho results column name 'motif_in_query' to 'motif_inside_subject_query_overlap'.
- Added interaction domain information to results (new columns: "InteractionDomainId", "InteractionDomainDescription", "InteractionDomainName").
- The regex string for regular expression matches was encapsulated as follows: "(?=(regex))" (instead of directly passing the regex string "regex") to enable capturing all occurrences of a motif when the motif length is variable and there are repeats in the sequence ([https://regex101.com/r/HUWLlZ/1](https://regex101.com/r/HUWLlZ/1)).
- [`gget setup`](./setup.md): Use the `out` argument to specify a directory the ELM database will be downloaded into.
- [`gget setup`](./setup.md): Use the `out` argument to specify a directory the ELM database will be downloaded into. Completes [this feature request](https://github.com/pachterlab/gget/issues/119).
- [`gget diamond`](./diamond.md): The DIAMOND command is now run with `--ignore-warnings` flag, allowing niche sequences such as amino acid sequences that only contain nucleotide characters and repeated sequences. This is also true for DIAMOND alignments performed within [`gget elm`](./elm.md).
- [`gget ref`](./ref.md) and [`gget search`](./search.md) back-end change: the current Ensembl release is fetched from the new [release file](https://ftp.ensembl.org/pub/VERSION) on the Ensembl FTP site to avoid errors during uploads of new releases.
- [`gget search`](./search.md):
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