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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog.

0.4.0 -

0.3.11 - 2021-03-18

  • Re-release for dependency updates

0.3.10 - 2021-03-18

Fixed

  • Certain errors in the search service now return error messages instead of a generic 500.

0.3.9 - 2021-10-04

Changed

  • The cigar field returned by the /families/{id}/relationships endpoint is now in the CIGAR format, not just CIGAR-inspired.

0.3.8 - 2021-07-16

Fixed

  • Fixed sorting by "type" or "subtype" fields in /families
  • FASTA sequences submitted for sequence search with blank sequence names (i.e. ">\nACGT") are assumed to have the name "Input", "Input_1", etc., instead of failing to return any results.
  • "Annotations" search results that overlapped the requested range but did not completely fit inside it were not included if they were on the '-' strand.

Added

  • /families/{id}/annotation_stats: New endpoint, providing the data from two endpoints in one query: /families/{id}/assemblies and /families/{id}/assemblies/{assembly_id}/annotation_stats.

0.3.7 - 2020-07-01

Fixed

  • Fixed calculation of species on /taxa/coverage endpoint.

0.3.6 - 2020-06-29

Added

  • /families (only in the "full" format) and /families/{id} include three new fields: source_method, source_method_description, and source_assembly. See api/swagger/swagger.yaml for more details.
  • /families/{id}/seed now reports the average kimura divergence of the alignment if available.
  • /families and /families/{id}/relationships have a new filter: include_raw
  • /families/{id}/relationships has a new filter: include
  • /taxa/coverage: New endpoint, reporting a count of leaf species which have Dfam entries assigned to them.

Changed

  • Some fields will be filled in with an accession where a "name" is usually specified, if the "name" is not available. This is done when the field is intended to be human-readable.
  • Results for the /families/{id}/relationship endpoint are now limited to 300.

0.3.5 - 2020-03-05

Fixed

  • "Method not allowed" errors respond with a 405 error instead of 500

0.3.4 - 2020-01-09

Fixed

  • "Annotations" search now includes hits that overlap the requested range, in addition to hits that are fully contained within the range.
  • Fixed a regression that caused /families with format=full to fail.

0.3.3 - 2019-11-04

Added

  • Added support for single sequence downloads in 'fasta' format: /family/{id}/sequence?format=fasta
  • Added support for bulk downloads in 'fasta', 'embl', and 'hmm' formats via /families. This supports the same filtering and sorting options as the existing JSON output formats ('full' and 'summary').

Changed

  • Queries to /families will now fail if too many results would be returned from one query.

Fixed

  • Attempts to download invalid formats respond with a 400 error instead of a 500
  • Citations will always be returned in the correct order

0.3.2 - 2019-06-20

Added

  • New endpoint '/taxa/{id}' to retrieve information on a single taxon
  • Family objects now include a 'version' field

Changed

  • Updated handling of seed region names and positions

Fixed

  • Nonexistent search jobs are properly caught and handled as a 404

0.3.1 - 2019-04-25

Fixed

  • Fix stockholm formatter seed regions with duplicated positions (e.g. chr:1-5:1-5)
  • Fix /families classification filter matching more than it was supposed to
  • Use the search start date instead of job start date to find search results
  • Use the SQL charset that matches our databases

0.3.0 - 2019-03-04

Added

  • Initial public release of the Dfam API.