malva.cellxmer module

malva.cellxmer.malva_to_cellxmer(kmer_index, count_at_most=10000, count_at_least=10, verbose=True)

malva.cellxmer.malva_to_filtered_cellxmer_chunked(kmer_index, count_at_most=10000, count_at_least=10, k_size=None, w_size=16, num_buckets=100000, chunk_size=10000000, temp_dir=None, verbose=True)

Process a malva index to create a filtered cell-by-bucket matrix in chunks following the same approach as the original implementation but with chunked processing.