·
13 commits
to master
since this release
See Patch for more details.
Still in testing - full characterization of annotation accuracy is not completed yet.
- Reworked the B-cell phylogeny algorithm
- Reworked inputs to BRILIA
- Set an incomplete annotation to those with CDR3 lengths <5 or >30 amino acid long, or with >15 nt deletions of V, D, or J gene edges
- Added more command-line features to search and process files
- Added fastq file alignment quality filters (MinQuality), which will set low-quality base read as wildcard "N"
- Added ability to use custom VDJ gene databases if fasta files are provided
- Added and fixed post-processing code (mergeSimilarSeq) to remove sequences that diff less than a Cutoff hamming distance (integer >= 1) or fraction (between 0 and 1).
- Added BRILIA test functions
PERFORMANCE IMPROVEMENTS
- Moved more function to C++ for speed enhancement
- Made annotation and plotting codes multi-threaded
- Added parallel computing progress tracker (ProgressTracker.m)