NEWS

immApex 1.7.1

PERFORMANCE

buildNetwork() now scales to large, clonally expanded repertoires. The C++ engine was rewritten around candidate generation instead of all-pairs comparison, with no new dependencies and identical edge output for the default settings:

Identical sequences collapse to one representative before any distance is computed, so clonal expansion no longer drives quadratic work.
Length and V/J blocking act as an index. Only length-compatible representatives in the same block are compared.
Levenshtein and Damerau use deletion-neighborhood (SymSpell) hashing for small edit distances, with Damerau indexed at radius 2k. Hamming uses pigeonhole segment indexing. Both fall back to length-blocked comparison outside their range.
Edges accumulate as integer node indices and gain their labels in R, which avoids building millions of barcode strings inside the parallel core.

Speedups range from roughly 2x on mixed repertoires with many V genes to about 70x when one block holds many unique sequences at a tight threshold.

NEW FEATURES

Added the expand argument to buildNetwork(). "clique" (default) materializes every pairwise edge and reproduces the exact edge multiplicity that community-detection clustering expects. "star" links identical sequences through a single hub and connects related groups hub to hub. "star" produces far fewer edges and preserves connected components exactly, so it is a large memory win when the downstream step depends on connectivity.

BUG FIXES

Fixed a banded Levenshtein error that dropped pairs whose only optimal alignment rides the band edge, including identical sequences at a tight normalized threshold. The boundary cell read the wrong diagonal value. The fix only recovers true edges and never removes valid ones.
Made the normalized-threshold cutoff robust to floating-point rounding so a normalized distance exactly equal to the threshold is kept, matching the documented inclusive behavior.

immApex 1.5.4

BUG FIXES

Fixed vignette build failure when IMGT network data is unavailable (e.g., on Bioconductor build servers)
Fixed operator precedence bug in inferCDR() reference validation check

immApex 1.5.3

UNDERLYING CHANGES

getIMGT() now uses immReferent as a backend for downloading and caching IMGT reference sequences
Removed frame, max.retries, and verbose parameters from getIMGT()
Added refresh parameter to getIMGT() for controlling cache behavior
Removed hash, httr, and rvest package dependencies (now handled by immReferent)
Replaced .parseSpecies() with .mapSpecies() for immReferent species name compatibility

immApex 1.5.2

improved error message for the propertyEncoder() function when the suggested Peptides package is not installed.

immApex 1.5.0

Bioconductor devel branch update to match versions

immApex 1.4.3

NEW FEATURES

The buildNetwork() function has been significantly enhanced to include:

Multiple distance metrics: Added support for five distance metrics via the dist_type parameter:
- "levenshtein" (default): Standard edit distance
- "hamming": Substitutions only (requires equal-length sequences)
- "damerau": Levenshtein with transpositions
- "nw": Needleman-Wunsch global alignment
- "sw": Smith-Waterman local alignment
Flexible normalization: New normalize parameter supports three modes:
- "none" (default): Raw distance values (backward compatible)
- "maxlen": Normalize by max(length(seq1), length(seq2))
- "length": Normalize by mean sequence length

immApex 1.3.7

UNDERLYING CHANGES

Ensure buildNetwork() returns a symmetric distance matrix and drops nonstructural zeros

immApex 1.3.6

UNDERLYING CHANGES

Rebuilt propertyEncoder() and onehotEncoder() to use C++ backend with encodeSequences.cpp
Rebuilt buildNetwork() via C++ integration (fastEditEdges.cpp)
Motif quantification in calculateMotif() use C++ (calculateMotif.cpp)
Reduce overall dependencies on external packages
Improved speed of generateSequences(), mutateSequences(), adjacencyMatrix(), tokenizeSequences(), geometricEncoder
Added group.by argument to getIR()
Defunct variationalSequences()
Removed keras3/tensorflow suggests/dependencies
Removed baslisk environment, python no longer required
Updated C++ backend to C++17
Robust checks before running getIMGT() for website functioning
Removing special unicode symbols

NEW FEATURES

calculateEntropy() added to calculate the positional entropy along a biological sequence
Added basic diversity metrics (exported) to support calculateEntropy()
calculateFrequency() added to calculate the positional frequency along a biological sequence
calculateMotif() added to get motif quantification of sequences
calculateGeneUsage() added for single/paired gene enumeration
Added scaleMatrix() for comprehensive scale/transformation functions
Added summaryMatrix() for fast summarization of matrix values

BUGS

Fixed NT position issue with inferCDR()
Fixed generateSequence() range issue for single-length sequences
Fixed binary frequency issue in positionalEncoder()
Fixed buildNetwork() for relative thresholding returns relative value

immApex 1.2.2

Updated unit tests and vignette check
Converted package to basilisk from reticulate

immApex 1.2.0

Update version for BioConductor release

immApex 1.0.5

UNDERLYING CHANGES

getIMGT() checks for availability of IMGT website
Expanded Unit Tests
Unit Tests and Vignette now evaluate for proper python installation overall

immApex 1.0.4

UNDERLYING CHANGES

Optional testthat variationalSequences() evaluate presence of Keras

immApex 1.0.3

UNDERLYING CHANGES

Drop evaluation of variationalSequences() example

immApex 1.0.2

UNDERLYING CHANGES

Vignette includes eval of keras installation for certain chunks

immApex 1.0.1

UNDERLYING CHANGES

Fix issue with optimizer call in variationalSequences()
Move package to keras3
Version Bump to be consistent with Bioconductor release

immApex 0.99.5

UNDERLYING CHANGES

Remove keras installation in vignette
Removed lazydata loading
Added @return to the data manual entries
Update stop message for propertyEncoder()
Removed set.seed from variationalSequences()
Added runnable example for variationalSequences()
Added better handling of no connection in getIMGT()
Added max.retries to getIMGT()
Updated testthat for new IMGT version

immApex 0.99.3

UNDERLYING CHANGES

Defining python version 3.10 for keras installation

immApex 0.99.2

UNDERLYING CHANGES

Added discrete check and install_keras() to vignette

immApex 0.99.1

UNDERLYING CHANGES

Added warning to getIMGT() to mention IMGT license on first use
import magrittr instead of dplyr
Fixed issue with license error
Added example to positionalEncoder()
Replaced discrete calling of "es =" in vignette
Update readme to include keras based installation
added set.seed() to vignette
added introduction section to vignette with mention of other packages
removed installation section from vignette (can't add BioC instructions until accepted)
Fixed rendering issue with the vignette
Subsampled example data and removed Omniscope example
Updated testthat for formatGenes() and inferCDR() for new example data
Reduced size of test data
Minimized usage of sapply() and X:Y per BiocCheck suggestions
Modified print() messages to messages()
Add verbose parameter to turn on/off processing steps
Added links for example data formats