Opened 10 years ago

#585 new optimization

optimize database sequence compression

Reported by: westram Owned by: devel
Priority: major Milestone:
Component: Library (DB) Version: SVN
Keywords: Cc:



  1. when copying an alignment, master sequence (MS) compression is NOT copied ⇒ destination alignment uses more space than source alignment
  2. when sequence data gets modified, MS compression is dropped


  1. copy MS information when copying alignment
  2. reuse previously used MS when compressing changed sequence

Special case:

  • when inserting/deleting columns, the MS could be adapted (=perform insert/delete there as well)

Possible optimization:

  • currently optimize uses the following steps:
    1. re-compress sequences w/o using MS
    2. delete old and create new MS
    3. re-compress sequences using MS
  • step 1. could be skipped by using 2 sets of MS and 2 separate 'compression mode' flags (currently always GB_COMPRESSION_SEQUENCE). optimize then would perform as:
    1. create new MS
    2. re-compress sequences using old MS to decompress and new MS to compress
    3. delete old MS

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