slowikj/seqR

Issues

• Finish README

  #54 opened 3 years ago by slowikj
  0

• Improve generic iterator implementation in the dictionary module

  #71 opened 3 years ago by slowikj
  1

• Document API

  #45 opened 3 years ago by slowikj
  0

• Reduce the package size

  #82 opened 4 years ago by slowikj
  0

• Add merging k-mer output matrices

  #78 opened 4 years ago by slowikj
  0

• Add default alphabet value "all"

  #84 opened 4 years ago by slowikj
  0

• Add param with_kmer_names

  #51 opened 4 years ago by slowikj
  0

• FASTA format support

  #80 opened 4 years ago by slowikj
  0

• Set an optimized dictionary for each Alphabet Encoding depending on the number of elements

  #29 opened 4 years ago by slowikj
  1

• Fix CI

  #52 opened 4 years ago by slowikj
  0

• Add fill or complete parameter to count_kmers

  #77 opened 4 years ago by michbur
  2

• Support tidysq sequences

  #38 opened 4 years ago by slowikj
  0

• Better hashing functions

  #7 opened 4 years ago by slowikj
  1

• Try to use optimized hash map

  #10 opened 4 years ago by slowikj
  2

• Extract hash type

  #67 opened 4 years ago by slowikj
  0

• Add specialized versions of input wrappers for sequential (not parallel) mode

  #62 opened 4 years ago by slowikj
  0

• Add a max_threads_num_param

  #32 opened 4 years ago by slowikj
  1

• Use a data structure to store common function params

  #58 opened 4 years ago by slowikj
  0

• Clean up package namespace: refactor C++ exported function names

  #53 opened 4 years ago by slowikj
  0

• Add parallel_mode param

  #59 opened 4 years ago by slowikj
  0

• Improve the performance for string matrix input

  #33 opened 4 years ago by slowikj
  3

• Prepare optimized and specialized variants of AlphabetEncoding for each input sequence type

  #60 opened 4 years ago by slowikj
  0

• Add window slide size param

  #57 opened 4 years ago by slowikj
  0

• Change the algorithm for positional k-mer space

  #55 opened 4 years ago by slowikj
  0

• GitHub Actions integration

  #48 opened 4 years ago by slowikj
  0

• Add verbose param

  #47 opened 4 years ago by slowikj
  0

• Add user interruption check

  #22 opened 4 years ago by slowikj
  0

• Determine the number and params (P, M) for hashing functions

  #8 opened 4 years ago by slowikj
  0

• Output matrix does not contain rows for the last input sequences without k-mers

  #40 opened 4 years ago by slowikj
  0

• Tidysq: make unpacking sequences parallel

  #14 opened 4 years ago by slowikj
  1

• Add count_multimers

  #35 opened 4 years ago by slowikj
  0

• Memory not mapped error

  #31 opened 4 years ago by slowikj
  0

• Final k-mer frequency result format

  #12 opened 5 years ago by slowikj
  1

• Process sequences in batches

  #16 opened 5 years ago by slowikj
  0

• Add BloomFilter to find k-mers

  #11 opened 5 years ago by slowikj
  0

• Performance of std::string

  #27 opened 5 years ago by slowikj
  0

• Count only k-mers that are in the provided input k-mer set

  #23 opened 5 years ago by slowikj
  0

• Wrap related input fields into structures in order to reduce the number of function's params

  #24 opened 5 years ago by slowikj
  0

• Extra param to find_kmers to specify a dictionary to store k-mers

  #25 opened 5 years ago by slowikj
  0

• Handle the case when gapped k-mer is longer than a sequence

  #26 opened 5 years ago by slowikj
  0

• Add param to find k-mers without counts

  #21 opened 5 years ago by slowikj
  0

• Tidysq: make sure that rowGetter create no copy of Rcpp::RawVector

  #15 opened 5 years ago by slowikj
  0

• Make columns in a result matrix compliant with biogram output

  #17 opened 5 years ago by slowikj
  0

• Nullable handling + delegation to a specialized method

  #13 opened 5 years ago by slowikj
  0

• tidySq integration

  #5 opened 5 years ago by slowikj
  0

• Better hash computation of a complex_hash (std::vector<int>)

  #9 opened 5 years ago by slowikj
  0

• C++ tests

  #6 opened 5 years ago by slowikj
  0