LexicMap v0.5.0

v0.5.0 - 2024-12-18

This version is compatible with indexes created by LexicMap v0.4.0, but rebuilding the index is recommended for more accurate results.

• New commands:
  • lexicmap utils remerge: Rerun the merging step for an unfinished index.
• lexicmap index:
  • Big genomes with thousands of contigs (big yet fragmented assemblies) are automatically split into multiple chunks, and alignments from these chunks will be merged.
  • Change the default value of --partitions from 1024 to 4096, which increases the seed-matching speed at the cost of 2 GiB more memory occupation.
    For existing lexicmap indexes, just run lexicmap utils reindex-seeds --partitions 4096 to re-create seed indexes.
  • Do not save seeds of low-complexity.
  • Fix high memory usage in writing seed data.
  • Change the default value of -c/--chunks from all available CPUs to the value of -j/--threads.
  • Change the default value of --max-open-files from 512 to 1024.
  • Add a new flag --debug.
• lexicmap search:
  • Improving chaining, pseudoalignment, and alignment for highly repetitive sequences.
  • More accurate chaining score with better chaining of overlapped anchors, this produces more accurate results with -n/--top-n-genomes:
    • Merging two overlapped non-gapped anchors into a longer one.
    • For these with gaps, only the non-overlapped part of the second anchor is used to compute the weight.
    • Using the score of the best chain (rather than the sum) for sorting genomes when using -n.
  • Fix positions and alignment texts for queries with highly repetitive sequences in end regions. #9
  • Skip seeds of low-complexity.
  • Change the default value of --max-open-files from 512 to 1024.
  • Change the default value of --align-band from 50 to 100.
  • Improve the speed of anchor deduplication, genome information extraction, and result ordering.
  • Improve the speed of chaining for long queries.
  • Improve the speed of seed matching when using -w/--load-whole-seeds.
  • Improve the speed of alignment, and reduce the memory usage.
  • Remain compatible after the change of lexicmap index.
  • Add a new flag --debug.
• lexicmap utils genomes:
  • Do not sort genome ids.
  • Add a header line and add another column to show if the reference genome is chunked.
• lexicmap utils subseq:
  • Remain compatible after the change of lexicmap index.
• lexicmap utils seed-pos:
  • Remain compatible after the change of lexicmap index, while histograms are plotted separately for multiple genome chunks.
• lexicmap utils reindex-seeds:
  • Change the default value of --partitions from 1024 to 4096.