Commits on Nov 5, 2020

1. Index input sequences and stream output sequences …

   Reduces memory needed by augur filter to a smaller constant value
   instead of loading all input sequences into memory once and then again
   when writing sequences out to disk. The primary improvements here are:
   
   1. Use a BioPython index data structure [1] that tracks where each
   sequence is on disk but does not load sequences into memory. This
   structure acts the same as the dictionary structure we originally used
   except sequences are loaded lazily when they are requested.
   
   2. Use an iterator to write sequences back to disk. BioPython's SeqIO
   write method accepts an iterator that allows us to stream sequences back
   to disk without first loading them into memory as a list of sequence
   objects.
   
   [1] http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec66

   

   huddlej committed Nov 5, 2020
   Configuration menu

   • View commit details
   • Copy full SHA for 9febe77
   • Browse repository at this point

   Copy the full SHA

   9febe77 View commit details

   Browse the repository at this point in the history