Feat@vtrack fft #29
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Feat@vtrack fft #29
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- Bumped package version to 4.3.8. - Introduced new virtual track functions: `kmer.fft`, `kmer.fft.peak`, and `kmer.fft.peak.power` for FFT analysis of kmer occurrence signals.
- Improved documentation for `kmer.count`, `kmer.frac`, and `kmer.fft` functions, clarifying the behavior of the `extend` parameter and window functions. - Added validation for the frequency parameter in `kmer.fft` to ensure it is between 0 and 0.5. - Updated the `get_kmer_signal` function to accept additional parameters for better signal processing. - Introduced comprehensive tests for kmer FFT functionality, covering various scenarios including different window functions and frequency validations.
- Replaced calls to `Rf_GetOption` with `Rf_GetOption1` for improved option handling in `rdbinterval.cpp`, `rdbutils.cpp`, and `TrackExpressionScanner.cpp`. - Updated the `gtrack_create_dense` function to use `isDataFrame` for data frame validation. - Added a compatibility definition for `isDataFrame` in `rdbutils.h` for R versions below 4.5.0.
…tibility macro - Changed the validation check in `gtrack_create_dense` to use `Rf_isDataFrame` for improved clarity and consistency. - Corrected the compatibility macro definition for `Rf_isDataFrame` in `rdbutils.h` to ensure proper functionality in R versions below 4.5.0.
- Added clarification on converting frequency to period in base pairs in the documentation for `kmer.fft.peak` and `kmer.fft.peak.power`. - Expanded the description of the `freq` parameter to include its relationship with the period and valid range.
- Added KISS FFT library to enhance FFT functionality in genomic sequence analysis. - Updated `KmerFFT` class to utilize KISS FFT for FFT computations, replacing the previous simple DFT implementation. - Enhanced documentation in `DESCRIPTION` and `README.md` to acknowledge the use of KISS FFT. - Introduced new header and source files for KISS FFT integration, ensuring proper configuration and memory management.
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- findListElementIndex returns -1 when parameters aren't found - Negative indices were used directly with VECTOR_ELT causing undefined behavior - Added proper index validation before accessing list elements - Required parameters (pssm, kmer, freq) now throw clear error messages when missing - Optional parameters (bidirect, extend, strand, window) gracefully handle missing values - Affects PWM, kmer.count, kmer.frac, and kmer.fft virtual track functions
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