v4.0.9

What's Changed

Functional changes:

• Creating release tag for v4.0.9 which includes base count aggregates

Full Changelog: v4.0.8...v4.0.9

Docker container:
https://github.com/formbio/laava/pkgs/container/laava/398147910?tag=4.0.9

v4.0.8

What's Changed

• Flipflop computation and performance optimization @beichen1024 in #122

New Contributors

• @beichen1024 made their first contribution in #122

Full Changelog: v4.0.7...v4.0.8

v4.0.7

What's Changed

• Revert "Fix flipflop test expectations" by @vijayformbio in #118
• Disable scAAV flipflop processing to prevent memory issues by @mcrocker-bioborg in #119
• adding lambda counts definitions by @alphabdiallo in #115
• Revert PR #107 flip/flop fixes until performance/correctness resolved by @dougnukem in #120
• Skip flip-flop analysis for scAAV vectors by @vijayformbio in #121

New Contributors

• @vijayformbio made their first contribution in #118

Full Changelog: v4.0.6...v4.0.7

v4.0.6

What's Changed

• Fix flipflop test expectations by @mcrocker-bioborg in #110

Full Changelog: v4.0.5...v4.0.6

v4.0.5

What's Changed

• Add comprehensive local testing framework with golden master verifica… by @mcrocker-bioborg in #106
• Centralize lint checking in Makefile and run on make test locally by @dougnukem in #109
• flip/flop fixes by @alphabdiallo in #107

New Contributors

• @mcrocker-bioborg made their first contribution in #106

Full Changelog: v4.0.4...v4.0.5

v4.0.4

Creating Laava Release v4.0.4

This release includes

1. fixes an issue found that was including duplicates being included in mutation calculations
2. enhances clarity on labels related to these mutational fix to help make clear what these numbers are intended to represent

Release v4.0.3

What's Changed

• Fixed docker permission issue when not running as root

v4.0.2

What's Changed

Functional changes:

• #98 Fixing multiprocessing output files issues

Full Changelog: v4.0.1...v4.0.2

Docker container:
https://github.com/formbio/laava/pkgs/container/laava/398147910?tag=4.0.2

v4.0.1

What's Changed

Functional changes:

• #94 Fixed sc-AAV itr-partial type classification to properly identify and classify itr-partial reads
• Bug fixes for chunking based on numCpus to ensure last chunk is within bounds
• Added configuration parameters to customize machine type, CPU count, and memory allocation --cpus=48 --memory=64GB
  ** Default settings now configurable: 8 CPUs, and 64GB memory

Full Changelog: v4.0.0...v4.0.1

Docker container:
https://github.com/formbio/laava/pkgs/container/laava/392266659?tag=4.0.1

v4.0.0

What's Changed

Functional changes:

• Handle mITR/wtITR directionality for scAAV classification via new input "mitr_label" (#70)
• Output aggregate summary tables for reporting (#67)
• Add version number to output metadata TSV (#72, #86)
• Handle effective_count correctly in aggregating plots (#68)

For developers:

• Expose "make test" at the top level of the repo (#89)
• Expose scAAV/tandem threshold parameter "min_supp_joint_coverage" (#89)
• Include aggregate-data TSVs in regression test suite (#86)
• Configure for compatibility with AWS and wrapper workflows (#86)

Additional smaller fixes: #74, #75, #77, #81, #83, #89, #92

Full Changelog: v3.0.0...v4.0.0