Comments (3)
The optimal, though less probable to achieve (however, still worth trying :) ), approach for this problem is to analyze the implementation of Rcpp::StringMatrix
in depth and try to create a thread-safe wrapper.
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A better, however still not optimal approach, is encoding instead of converting strings elements.
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In fact, it seems more efficient just not to use parallel version. This hypothesis should be tested.
The hypothesis will be tested in #62
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Related Issues (20)
- Document API
- Add verbose param
- GitHub Actions integration
- Add param with_kmer_names
- Fix CI
- Clean up package namespace: refactor C++ exported function names
- Finish README
- Change the algorithm for positional k-mer space
- Add window slide size param
- Use a data structure to store common function params
- Add parallel_mode param
- Prepare optimized and specialized variants of AlphabetEncoding for each input sequence type
- Add specialized versions of input wrappers for sequential (not parallel) mode
- Extract hash type
- Improve generic iterator implementation in the dictionary module HOT 1
- Add fill or complete parameter to count_kmers HOT 2
- Add merging k-mer output matrices
- FASTA format support
- Reduce the package size
- Add default alphabet value "all"
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