microhapdb - MicroHapDB 0.11

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 match to the correct marker definition (see #150).

- Python
Published by standage over 2 years ago

microhapdb - MicroHapDB 0.10.1

Fixed

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

- Python
Published by standage over 2 years ago

microhapdb - MicroHapDB 0.10

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).

- Python
Published by standage over 2 years ago

microhapdb - MicroHapDB 0.9

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).

- Python
Published by standage over 2 years ago

microhapdb - MicroHapDB 0.8.2

Fixed

• Test suite execution bug.

- Python
Published by standage over 3 years ago

microhapdb - MicroHapDB 0.8.1

Fixed

• Bundling of files used for automated test suite.

- Python
Published by standage over 3 years ago

microhapdb - MicroHapDB 0.8

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).

- Python
Published by standage over 3 years ago

microhapdb - MicroHapDB 0.7

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).

- Python
Published by standage about 4 years ago

microhapdb - MicroHapDB 0.6

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).

- Python
Published by standage over 5 years ago

microhapdb - MicroHapDB 0.5

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).

- Python
Published by standage about 6 years ago

microhapdb - MicroHapDB 0.4.3

Fixed

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

- Python
Published by standage over 6 years ago

microhapdb - MicroHapDB 0.4.2

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).

- Python
Published by standage over 6 years ago

microhapdb - MicroHapDB 0.4.1

Fixed

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

- Python
Published by standage over 6 years ago

microhapdb - MicroHapDB 0.4

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).

- Python
Published by standage over 6 years ago

microhapdb - MicroHapDB 0.3

Added

• Microhaps and limited allele frequency data from LOVD (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).

- Python
Published by standage almost 7 years ago

microhapdb - MicroHapDB 0.2

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

- Python
Published by standage about 7 years ago

microhapdb - MicroHapDB 0.1.2

Fixed a bug with testing the installed package.

- Python
Published by standage over 7 years ago

microhapdb - MicroHapDB 0.1.1

Fixed a bug with distributing non-code files.

- Python
Published by standage over 7 years ago

microhapdb - MicroHapDB 0.1

Initial release!

- Python
Published by standage over 7 years ago