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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

[Unreleased]

Fixed

  • Debugged a test that counts observed haplotypes (#154).
  • Replaced global pooled Ae values with 26-population average as the default Ae reported (#155).
  • Replaced deprecated pkg_resources module with importlib.resources (#156).
  • Upgraded versioneer to a Python 3.12+ compatible version (#156).

[0.11] 2023-10-25

Added

  • A new table flagging markers with repetitive content (see #147).
  • A new column in the microhapdb.frequencies table containing the number of observed haplotypes used to compute frequency estimates for each population group (see #151).

Changed

  • Merged RSIDs resolved during database build now propagated to the final marker definition (see #149).

Fixed

  • Added manual and automated fixes to ensure frequencies are formatted correcly and matche to the correct marker definition (see #150).

[0.10.1] 2023-10-13

Fixed

  • Bug with offsets table (marker --format=offsets) when multiple markers are defined for a locus (#144).

[0.10] 2023-09-15

Added

  • Marker definitions for NimaGen 29-plex (see #134).
  • 50 marker definitions from Zhang et al 2023 (see #136).
  • 191 marker definitions from Du et al 2023 (see #137).
  • Jupyter notebook for plotting database growth over time (see #135).

Changed

  • Cleanup of database build code (see #133).
  • Improved marker detail view now includes locus, marker, synonym, and source info (see #138).
  • Updated documentation (see #139, #142).

Fixed

  • Off-by-one errors in Fan 2022 marker definitions (see #140).

[0.9] 2023-07-03

Added

  • Italian population frequencies for 98 markers from Turchi et al 2019 (see #107).
  • 21 marker definitions and population frequences from Zou et al 2022 (see #109).
  • Check for overlapping microhaps from different sources during the database build (#112).
  • Over 1,000 marker definitions from four whole-genome screens from Yu et al 2022 (see #115, #118, #128).
  • New nomenclature module for parsing and validating microhap identifiers (see #119).
  • New summarize subcommand for summarizing MicroHapDB database contents (see #120).
  • 1,000 marker definitions from Zhu et al 2023 (see #125, #131).
  • New check during database build time to make sure that markers sharing the same name actually occupy the same locus (see #128).

Changed

  • Overhaul of the marker table structure and database build procedure (see #106, #111, #112).
  • Use Byrska-Bishop 2022 instead of Auton 2015 for main frequency and Ae calculations (see #106, #112, #114, #130).
  • Marker FASTA output now produces a single sequence per locus, even when multiple markers at a locus are defined (#124).

[0.8.2] 2022-11-21

Fixed

  • Test suite execution bug.

[0.8.1] 2022-11-21

Fixed

  • Bundling of files used for automated test suite.

[0.8] 2022-11-21

Added

  • 25 marker definitions from Sun et al 2020 (see #87).
  • 23 marker definitions from Jin et al 2020 (see #89).
  • 20 marker definitions from Kureshi et al 2020 (see #90).
  • GRCh38 offsets to microhapdb marker --format=offsets (see #92).
  • 59 marker definitions from Wu et al 2021 (see #96).
  • 22 marker definitions from Fan et al 2022 (see #97).
  • New sphinx-based documentation suite hosted on ReadTheDocs.org (see #101).

Changed

  • Minor improvements to database build and corresponding documentation (see #88).
  • Major overhaul of the Python API (see #99).

Fixed

  • Bug with dereferencing IDs and ID cross-references (see #99, #100).

[0.7] 2022-01-20

Added

  • Markers and population frequency data (1000 Genomes and proprietary) for the mMHseq 90-plex panel (see #68).
  • New --extend-mode option when displaying markers in fasta or detail mode (see #72).
  • New options for preparing MicroHapDB data for import into MicroHapulator (see #80).
  • New option for preparing MicroHapDB frequency data for import into probgen tools like LRMix Studio or EuroForMix (see #82).

Changed

  • Support for pandas>=1.2 added, support for Python 3.6 dropped (see #74).
  • The --marker and --population flags for microhapdb frequency now support multiple arguments (see #81).

Fixed

  • Error message when detail view is requested for a marker without frequency information (see #67).
  • Problematic haplotype frequencies for 4 mMHseq markers including SNPs whose rsIDs are not present in the original 1KGP data (see #73).

[0.6] 2020-06-25

Added

  • Added F_ST (fixation index) to the markers table (see #59, #62, #63).
  • Added the ability to swap out population-specific Ae values for the default 26-population average (see #63).
  • Support for GRCh37 (see #64).

Changed

  • Various updates to documentation (see #60).
  • Cosmetic updates to "marker --detail" (see #61).
  • Refactoring of database build: cleanup using Pandas, reorganization for GRCh37 support (see #62, #64).

[0.5] 2020-02-13

Added

  • Added 10 marker definitions from Voskoboinik et al 2018 (see #47).
  • Added 118 marker definitions from de la Puente, Phillips, et al 2020 (see #49, #54).
  • Added microhap frequency estimates for 26 global populations to all markers from the 1000 Genomes Project Phase 3 dat (see #55).
  • Added I_n (informativeness for assignment) scores to each marker (see #56).

Fixed

  • Removed duplicate entry for marker mh11CP-004 (see #46).
  • Corrected marker name from mh05KK-058 to mh15KK-058 (see #46).
  • Corrected erroneous rsID assignments for van der Gaag 2018 markers (see #46).

Changed

  • 26 global populations from the 1000 Genomes Project migrated from ALFRED data source to a dedicated 1KGP data source (see #45).
  • Dropped Travis CI configuration (see #47).
  • Changed default delta from 25 to 10 and default minlength from 250 to 80 (see #52).

[0.4.3] 2019-11-05

Fixed

  • Squashed a bug with package data not being installed correctly.

[0.4.2] 2019-11-05

Changed

  • Some aspects of panel design and definition migrated from MicroHapulator to MicroHapDB (see #34, #35).
  • Minor changes to TargetAmplicon class to support MicroHapulator (see #36).

[0.4.1] 2019-10-22

Fixed

  • Corrected a copy/paste error (see #33).

[0.4] 2019-10-22

Added

  • Marker definitions and allele frequencies for a 40 microhap panel presented at ISFG 2019 (see #25).
  • Marker definitions and allele frequencies for 27 microhaps published in a 2015 Legal Medicine paper (see #31).
  • Marker definitions and allele frequencies for 11 microhaps published in a 2019 FSI: Genetics paper (see #32).

Changed

  • Replaced all references to locus and loci with marker and markers in the main code base (see #23).
  • Huge overhaul to the database build procedure, the CLI, and the Python API (see #27).

[0.3] 2019-05-02

Added

  • Marker definitions and allele frequency data for 16 microhaps from a 2018 FSI: Genetics paper (see #14).
  • Function to compute SNP positions from microhap locus ID (see #18).
  • A function to compute standard internal MicroHapDB ID for a single label or list of labels (see 9ec1e93735); any combination of ALFRED, LOVD, and MicroHapDB identifiers are valid input.

Changed

  • Replaced pip/PyPI installation instructions with bioconda installation instructions (see #14).

Fixed

  • Corrected DB build and coordinates (see #15).

[0.2] 2018-12-06

Changed

  • New command-line interface.
  • New Python API.
  • New database based on an updated table of 198 microhaplotype loci across 96 populations from ALFRED.

[0.1.2] 2018-10-10

Fixed a bug with testing the installed package.

[0.1.1] 2018-10-10

Fixed a bug with distributing non-code files.

[0.1] 2018-10-10

Initial release!