LexicMap v0.3.0

v0.3.0 - 2024-05-14

• lexicmap index:
  • Better seed coverage by filling sketching deserts.
  • Use longer (1000bp N's, previous: k-1) intervals between contigs.
  • Fix a concurrency bug between genome data writing and k-mer-value data collecting.
  • Change the format of k-mer-value index file, and fix the computation of index partitions.
  • Optionally save seed positions which can be outputted by lexicmap utils seed-pos.
• lexicmap search:
  • Improved seed-chaining algorithm.
  • Better support of long queries.
  • Add a new flag -w/--load-whole-seeds for loading the whole seed data into memory for faster search.
  • Parallelize alignment in each query, so it's faster for a single query.
  • Optional outputing matched query and subject sequences.
  • 2-5X searching speed with a faster masking method.
  • Change output format.
  • Add output of query start and end positions.
  • Fix a target sequence extracting bug.
  • Keep indexes of genome data in memory.
• lexicmap utils kmers:
  • Fix a little bug, wrong number of k-mers for the second k-mer in each k-mer pair.
• New commands:
  • lexicmap utils gen-masks for generating masks from the top N largest genomes.
  • lexicmap utils seed-pos for extracting seed positions via reference names.
  • lexicmap utils reindex-seeds for recreating indexes of k-mer-value (seeds) data.
  • lexicmap utils genomes for list genomes IDs in the index.