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Restructure repo so it's clear which approach is using the streaming, and which is using Bloom filters #18

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dkoslicki opened this issue Feb 6, 2020 · 0 comments
Open

Restructure repo so it's clear which approach is using the streaming, and which is using Bloom filters #18

dkoslicki opened this issue Feb 6, 2020 · 0 comments
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good first issue

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@dkoslicki
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The Bloom filter approach (presented in this paper) corresponds to:

  1. MakeDNADatabase.py
  2. QueryDNADatabase.py
  3. MakeNodeGraph.py

The new (as of yet unpublished) implementation that uses ternary search trees and streaming consists of

  1. MakeStreamingDNADatabase.py
  2. MakeStreamingPrefilter.py
  3. StreamingQueryDNADatabase.py
  4. StreamingQueryDNADatabase_queue.py (depreciated)

Need to clarify this in the repo structure, as well as Update the documentation
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