MicroHapulator 0.8.4

Fixed

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

MicroHapulator 0.8.3

Fixed

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

MicroHapulator 0.8.2

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).

MicroHapulator 0.8.1

Changed

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

MicroHapulator 0.8

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).

MicroHapulator 0.7.2

Fixed

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

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

• 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).

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

• 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).