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@Donaim Donaim released this 01 Nov 22:00
· 269 commits to master since this release
v7.17.1
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Donaim
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Learn about vigilant mode.

New Contig Stitching Algorithm

The updated contig stitching algorithm in MiCall now stitches contigs directly, avoiding reliance on reference genome regions, which improves accuracy. Both stitched and unstitched files support workflows like the proviral pipeline. Diagnostic tools include SVG visualizer plots and log files for transparency. More details at issue 1030.

Update to HIVdb v9.4

MiCall now uses HIVdb v9.4, enhancing resistance interpretation. Key updates include score changes for NRTI drugs (ABC, AZT, TDF, 3TC/FTC) and revised resistance profiles for Doravirine. More details at issue 884.

Simplified Coverage Plots

Improvements to coverage plots include the removal of V3 overlaps, external legends, and visual markers for mutations, reducing clutter and enhancing readability. More details at issue 537.

Fixes to Concordance Plots

Errors in concordance plots have been fixed, addressing issues related to contigs ending with large insertions, alignment corrections, and small alignment errors. Details in issues 887, 963, and 899.

Updates to proviral Pipeline Integration

Enhancements include HIVIntact backend support, automatic downloading of proviral_landscape.csv, and suspension of proviral uploads to QAI to prevent failures. More details in issues 994, 984, and 886.

New Project Code: HIV-AD

Introduced HIV-AD, modeled after the HIV-GHA project, involving cloning the project code, updating PCR primers, and QAI implementation. Details at issue 998.

Code Quality Improvements

Enhancements include:

  1. Linting Support: Added flake8 for code quality (pull 1055).
  2. Type Annotations: Introduced mypy for early error detection (pull 1035).
  3. Dependency Updates: Updated major dependencies.
  4. OS Update: Moved to Debian 12 for Singularity images (pull 1018).
  5. New Tools and Features: Added aln2counts_simplify.py1 and streamlined aligntools (pull 1023, 1068).
  6. Floating Point Handling: Improved update_qai.py2 reliability (pull 1075).
  7. Split Singularity Test: Separated Singularity test in CI (pull 1080).

Explore the GitHub milestone for an overview: milestone.

Additional resources:

  1. aln2counts_simplify.py here. ↩

  2. update_qai.py here. ↩

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