Releases: bioforensics/MicroHapulator
Releases · bioforensics/MicroHapulator
MicroHapulator 0.7.2
MicroHapulator 0.7.1
Fixed
- Updated MANIFEST.in, setup.py (e143d11).
MicroHapulator 0.7
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).
Changed
MicroHapulator 0.6.1
Fixed
- Bug with Snakefile not being included in package data.
MicroHapulator 0.6
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
MicroHapulator 0.5
Added
- New
--base-qual
parameter formhpl8r 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
- 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, c98bf6c). - Replaced the "ObservedProfile" terminology with the more appropriate "TypingResult" (#99).
- Documentation now uses Sphinx to render markdown as HTML (c98bf6c, #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).
MicroHapulator 0.4.1
Fix minor metadata typo
MicroHapulator 0.4
Added
- New
contain
module for calculating the proportion of alleles from one sample present in another sample (see #41). - New
--dry-run
mode forsim
andmixture
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 newseq
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 onProfile
objects (see #70).
Removed
MicroHapulator 0.3
MicroHapulator 0.2
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 1b61c59).
Fixed
- Corrected usage statement for
mhpl8r contrib
(see #31).