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Commits on Jan 14, 2019
  1. Solves recent typo

    lmrodriguezr committed Jan 14, 2019
    Just introduced in 4e969e6
  2. More efficient multi-threading of cleanup-databases.rb

    lmrodriguezr committed Jan 14, 2019
Commits on Dec 18, 2018
  1. Minor updates on daemon loading

    lmrodriguezr committed Dec 18, 2018
Commits on Dec 11, 2018
  1. Avoid re-scheduling previous jobs when daemon loads status

    lmrodriguezr committed Dec 11, 2018
Commits on Dec 10, 2018
  1. Pushed gem v0.3.6.3

    lmrodriguezr committed Dec 10, 2018
  2. Added CLI support for API Keys

    lmrodriguezr committed Dec 10, 2018
  3. Adds support for NCBI API Keys

    lmrodriguezr committed Dec 10, 2018
  4. Resolve bug just introduced

    lmrodriguezr committed Dec 10, 2018
  5. Correct typo (just introduced)

    lmrodriguezr committed Dec 10, 2018
  6. Rescue query distances run when ANI clade is not found

    lmrodriguezr committed Dec 10, 2018
  7. Daemon: Additional logs when loading previous status

    lmrodriguezr committed Dec 10, 2018
Commits on Dec 8, 2018
  1. Solved minor bug

    lmrodriguezr committed Dec 8, 2018
    This was causing distances to not explore the ANI clade of the closest
    relative in queries
  2. Database cleanup moved to :haai_distances

    lmrodriguezr committed Dec 8, 2018
Commits on Dec 7, 2018
  1. Removes requirement for ANIsp expansion in query distances

    lmrodriguezr committed Dec 7, 2018
Commits on Dec 6, 2018
  1. Reduce graphical abstract size

    lmrodriguezr committed Dec 6, 2018
  2. Adds graphical abstract to README

    lmrodriguezr committed Dec 6, 2018
  3. miga init now uses . instead of source

    lmrodriguezr committed Dec 6, 2018
    - This change makes it compatible with POSIX sh (e.g, ash and dash).
    - Close #60
    - Pushed gem v0.3.6.2
Commits on Dec 5, 2018
  1. Now the daemon takes over where a previous instance left off

    lmrodriguezr committed Dec 5, 2018
Commits on Dec 2, 2018
  1. Distances improved and style changes

    lmrodriguezr committed Dec 2, 2018
    Adds checkpoint so hAAI-only runs still save the AAI database
Commits on Nov 30, 2018
  1. Calculates ANI95 medoids in all projects

    lmrodriguezr committed Nov 30, 2018
Commits on Nov 29, 2018
  1. Important typo affecting :clade_finding and :subclades

    lmrodriguezr committed Nov 29, 2018
    gem v0.3.6.1 pushed
  2. Doesn't calculate ANI95-clade medoids for clade projects

    lmrodriguezr committed Nov 29, 2018
    AAI distance matrix not available for these projects
Commits on Nov 28, 2018
  1. Database cleanup is now centralized in :clade_finding

    lmrodriguezr committed Nov 28, 2018
    The previous approach cleaned one by one as part of `:stats`. The
    advantages with the current approach are reduced overhead/latency and
    streamlined updates
  2. Clade finding now uses ANI95 clades

    lmrodriguezr committed Nov 28, 2018
    - Removes `G` headers from ANI95 and AAI90 clade files
    - New `:medoids_ani95` file with ANI95 clade medoids
    - `:clade_finding` only runs on ANI95 medoid datasets
    - ANI is now calculated for all pairs with ANI ≥ 85% (it was 90% before)
    - Gem v0.3.6.0 pushed
  3. Prevents data loss from mirrored comparisons

    lmrodriguezr committed Nov 28, 2018
  4. Mirrored AAI/ANI values now saved to the individual databases

    lmrodriguezr committed Nov 28, 2018
Commits on Nov 18, 2018
  1. Minor changes release

    lmrodriguezr committed Nov 18, 2018
    - Gem v0.3.5.1 pushed
Commits on Nov 13, 2018
  1. Efficiency improved

    lmrodriguezr committed Nov 13, 2018
    Profiling revealed that a large portion of dataset listing (>75%) was
    used by `Array#include?`, and an additional 20% by the child
    `String#==`, so I’m using Hash lookup instead
  2. Resolves distances cleaning issue

    lmrodriguezr committed Nov 13, 2018
    query and inactive datasets we allowed in the final distance matrices
Commits on Nov 6, 2018
  1. Solves non-root links for GitBook

    lmrodriguezr committed Nov 6, 2018
  2. Solves root links in GitBook

    lmrodriguezr committed Nov 6, 2018
  3. manual test for gitbook

    lmrodriguezr committed Nov 6, 2018