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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]

Changed

  • Intermediate FASTQ files are now bgzip compressed to reduce storage requirements (#189).
  • Colons are now used instead of commas to separate SNP alleles in microhap alleles (#192).
  • Implemented Python 3.12 support by integrating happer package and increasing minimum version of MicroHapDB dependency (#193).
  • Updated working directory organization to provide additional structure (#194).

Fixed

  • Bug with handling marker vs. locus identifiers when running mhpl8r seq (#190).
  • Bug with writing output to terminal for some commands (#191).

[0.8.4] 2024-09-16

Fixed

  • Resolved a bug with the test suite (#187).

[0.8.3] 2024-09-16

Fixed

  • Resolved a bug with Table 4.4 in the final report.

[0.8.2] 2024-09-16

Changed

  • Alignment gaps are now marked instead of ignored (#185).
  • Tables were added to the final report to list markers with large numbers of discarded reads or reads containing gaps (#186).

[0.8.1] 2024-09-12

Changed

  • Updated the working directory structure so report is more easily shared (#181).
  • Replaced BWA MEM with Minimap2 for read alignment (#182).

[0.8] 2024-07-23

Added

  • Filtering of reads with too many ambiguous bases (#165).
  • Filtering of reads below a minumum length (#173).

Changed

  • Smart handling of multiple markers at a single locus implemented for type and pipe (#158).
  • Replaced parsers module with a MicrohapIndex class and supporting classes (#158).
  • Numerous updates to the mhpl8r pipe HTML report
    • Replaced read length distubition histograms with ridge plots (#167).
    • Replaced read QC donut plots with a stacked bar chart (#168, #177).
    • Replaced FastQC report links with MultiQC link (#169).
    • Revised report text, added figure captions and table titles (#172).
    • Streamlined the Python code responsible for generating the report (#175, #177, #180).
  • GRCh38 coordinates are now mandatory in marker definitions (#176).
  • Jijna2 sub-templates added to handle differences in the report for single ended versus paired end reads (#179).

Fixed

  • Bug with inconsistent sorting of read counts for interlocus balance (#159).
  • Bug with counting repetitive reads (#163).
  • Typing rate display in report (#174).

[0.7.2] 2022-10-12

Fixed

  • Resolved bug with lexicographical sorting of numeric data in mhpl8r pipe report (#156).

[0.7.1] 2022-09-20

Fixed

  • Updated MANIFEST.in, setup.py (6bf4533).

[0.7] 2022-09-19

Added

  • Profiles compatible with probgen programs now included in mhpl8r pipe output (#135).
  • Haplotype call plots now included in the mhpl8r pipe HTML report (#136).
  • New offtarget module to count reads that map to off-target loci in GRCh38 (#143, #153).
  • Added typing rate and mapping rate information per marker to the main mhpl8r pipe HTML report (#146).
  • Added marker detail page to the mhpl8r pipe HTML report (#146, #151).
  • Implemented support for single-end reads with mhpl8r pipe (#147).
  • Added donut plots to HTML report (#157)

Changed

  • Exposed static and dynamic threshold configuration to mhpl8r pipe CLI (#135, #153).
  • Updated plot colors in the mhpl8r pipe HTML report (#139).
  • Updated mhpl8r pipe HTML report to conditionally plot read length histograms or tables depending on uniformity (#140).

[0.6.1] 2022-04-27

Fixed

  • Bug with Snakefile not being included in package data.

[0.6] 2022-04-27

Added

  • New API and CLI entry points for computing and visualizing heterozygote balance (#122, #131).
  • New typing_rate method for the TypingResult class (#127).
  • New API function for plotting distribution of read lengths (#128).
  • New CLI entry point for downloading GRCh38 (#130).
  • New end-to-end microhap analysis pipeline and report (#129, #132).

Changed

  • Interlocus balance code updated to support generating high-resolution graphics and performing a chi-square goodness-of-fit test (#121, #131, #132).

Fixed

  • Bug with filtering/genotype calling for markers with no valid reads (#123).
  • Set 0.01 as a more reasonable default frequency for rare alleles than 0.001 (#131, #132).

[0.5] 2022-01-20

Added

  • New --base-qual parameter for mhpl8r type to set the minimum required base quality when iterating over reads in a pileup (#83).
  • New mhpl8r balance subcommand for calculating and visualizing interlocus balance (#85).
  • Users can now supply marker definitions, frequences, and reference sequences as TSV/FASTA files instead of MicroHapDB references (#93).
  • Configuration file examples in microhapulator/data/configs/ (#105).
  • New mhpl8r filter subcommand with support for marker-specific thresholds (#113, #114).
  • New mhpl8r convert subcommand for converting genotype calls into a format compatible with probgen tools such as LRMix Studio and EuroForMix (#115).

Changed

  • Updated mybinder demo (see #69, #110, #113).
  • Simulated Illumina sequencing now uses 1 thread by default, which paradoxically leads to better performance (#71).
  • Moved panel definition code moved out of the core code and into dedicated notebooks (#74).
  • Replaced MissingBAMIndexError with BAM auto-indexing code (#78).
  • Improved read names and choice of interleaved or paired output for mhpl8r seq (#80).
  • Updated filtering of haplotype calls / typing results
    • Replaced --threshold argument with --static and --dynamic, disabled both by default (#82, #83).
    • Split mhpl8r type subcommand into type and filter, with --static and --dynamic arguments only relevant to the latter (#113).
  • Changed the default pysam pileup max_depth parameter, overriding 8000 with 1e6 and exposing as a CLI parameter (#87, #113).
  • Removed dependency on MicroHapDB for marker definitions, frequencies, and sequences (#93).
  • Refactored CLI and Python API, adding new microhapulator.api module to serve as main entry point (#98, c98bf6c78ef4).
  • Replaced the "ObservedProfile" terminology with the more appropriate "TypingResult" (#99).
  • Documentation now uses Sphinx to render markdown as HTML (c98bf6c78e, #101, #102, #105, #106, #110).
  • Updated JSON schema for simulated profiles and typing results (#109).

Fixed

  • Corrected a bug with Fastq headers in mhpl8r seq module (#71).
  • Corrected a bug resulting from attempting to do set operations on None (#75).
  • Corrected a bug with RMP implementation (#86).
  • Set minimum versions for runtime dependencies (#97).
  • Corrected the --dynamic filter to operate on total haplotype counts rather than average counts (#114).

[0.4.1] 2019-11-06

Fix minor metadata typo

[0.4] 2019-11-05

Added

  • New contain module for calculating the proportion of alleles from one sample present in another sample (see #41).
  • New --dry-run mode for sim and mixture modules (see #41).
  • New prob module for calculating likelihood ratio tests based on the random match probability (see #43).
  • New seq module focused entirely on sequencing samples where profiles have already been simulated (see #45).
  • New mix module for merging simulated profiles into a simulated mixture sample profile (see #45).
  • New unite module for "mating" two profiles to create a simulated "offspring" profile (see #47).
  • New diff modfule for showing the differences between two profiles (see #58, #60).

Changed

  • Huge refactoring effort to accommodate for recent changes to MicroHapDB's Python API (see #66).
  • The sim module no longer performs simulated sequencing (now handled by new seq module) and instead focuses entirely on haplotype simulation (see #45).
  • The type module now dynamically selects either an automatic threshold or a fixed threshold based on effective coverage (see #51, #61).
  • Moved simulation scripts to notebook directory, reimplemented as a Snakemake workflow (see #50, #57, #59).

Fixed

  • Corrected a bug in the USA panel code ensuring that all loci have allele frequency data for all relevant populations (see #56).
  • Corrected a problem with the contrib API that prevented it from working directly on Profile objects (see #70).

Removed

  • Dropped the mixture module, whose functionality is now covered by the more granular sim, mix, and seq modules (see #45).
  • Dropped the LocusContext class in favor of MicroHapDB's TargetAmplicon class designed for a similar purpose (see #67).

[0.3] 2019-06-06

Added

  • New interactive demo using Jupyter notebook and mybinder.org (see #32).
  • Scripts for simulating 8k individuals with demographics roughly matching those of the U.S.A. (see #13).

Changed

  • Updated dist and genotype modules to better support equality and distance comparisons between simulated and observed genotypes (see #34).
  • Simulated and observed genotype data now use a single unified JSON representation, enforced by JSON schema validation (see #38).

[0.2] 2019-05-21

Added

  • New getrefr module for installing human reference genome (see #30).
  • Improved error handling related to BAM index files (see #31).

Changed

  • Replaced pip/PyPI installation instructions with bioconda installation instructions (see 1b61c59200).

Fixed

  • Corrected usage statement for mhpl8r contrib (see #31).

[0.1.3] 2019-05-14

  • mark failing test
  • exclude __init__.py from test invocation

[0.1.2] 2019-05-07

Updating file manifest, troubleshooting bioconda build.

[0.1.1] 2019-05-07

Minor fix to setup.py for distribution purposes.

[0.1] 2019-05-02

Initial release of MicroHapulator!

Command-line entry point: mhpl8r Command-line operations:

  • contrib: estimate number of contributors in a sample
  • dist: compute naive Hamming distance between two sample genotypes
  • mixture: simulate a multiple-contributor sample
  • refr: retrieve reference genome cutouts for a specified microhap panel
  • sim: simulate a single-contributor sample
  • type: infer genotype from mapped reads