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refactor the sbt_gather code to be sane(r) #136

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merged 4 commits into from Feb 22, 2017

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ctb
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@ctb ctb commented Feb 21, 2017

note, PR into #135.

also fixes a bug in find_best when threshold is set to 0.

  • add test for 0 threshold

  • Is it mergeable?
  • make test Did it pass the tests?
  • make coverage Is the new code covered?
  • Did it change the command-line interface? Only additions are allowed
    without a major version increment. Changing file formats also requires a
    major version number increment.
  • Was a spellchecker run on the source code and documentation after
    changes were made?

@brooksph
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This works!

running sourmash subcommand: sbt_gather

loaded query: all.fna... (k=21, DNA)
query signature has max_hash: 1844674407370955
found: 1.00 0.31 NC_000853.1 Thermotoga maritima MSB8 chromosome, complete genome
found: 0.90 0.28 NC_011978.1 Thermotoga neapolitana DSM 4359, complete genome
found: 1.00 0.26 NC_002163.1 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 chromosome, complete genome
found: 0.48 0.15 NC_009486.1 Thermotoga petrophila RKU-1, complete genome
found 4 matches total
the recovered matches hit 0.0% of the query

Composition:
1.00 NC_002163.1 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 chromosome, complete genome
1.00 NC_000853.1 Thermotoga maritima MSB8 chromosome, complete genome
1.00 NC_011978.1 Thermotoga neapolitana DSM 4359, complete genome
1.00 NC_009486.1 Thermotoga petrophila RKU-1, complete genome

@brooksph brooksph merged commit 43ca903 into report/full_genome_fraction Feb 22, 2017
@luizirber luizirber added the sbt label May 4, 2017
@luizirber luizirber added this to Done in sourmash 2.0 May 19, 2017
@luizirber luizirber removed this from Done in sourmash 2.0 May 19, 2017
@luizirber luizirber deleted the refactor/full_genome_fraction branch October 30, 2017 01:18
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3 participants