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Add Sequence Bloom Tree-based search into sourmash #45

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merged 77 commits into from Dec 29, 2016

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ctb commented Nov 10, 2016

Makes use of @luizirber code from https://github.com/luizirber/2016-sbt-minhash to provid indexing and search subcommands.

Interesting question to ask: should we copy the SBT files into this repo? We could either have the SBT stuff be another project or we could develop it as part of sourmash until we have reason to split it off. Alternatively we could develop the SBT code as part of khmer (again, until we have reason to split).

  • 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?
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The lazy loading hack (5a78330) really speeds things up @luizirber!

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ctb commented Nov 18, 2016

The lazy loading hack (5a78330) really speeds things up @luizirber!

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Instead of merging back the sbt stuff, what do you think about developing it here in sourmash? No point in keep things synchronized in two different places...

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luizirber commented Nov 28, 2016

Instead of merging back the sbt stuff, what do you think about developing it here in sourmash? No point in keep things synchronized in two different places...

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ctb commented Nov 29, 2016

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The review will happen here (eventually =P), no need to split things. I'll post a warning on the old repo pointing to sourmash (and sbt_gather isn't really part of the sbt/sbtmh codebase anyway).

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luizirber commented Nov 29, 2016

The review will happen here (eventually =P), no need to split things. I'll post a warning on the old repo pointing to sourmash (and sbt_gather isn't really part of the sbt/sbtmh codebase anyway).

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ctb commented Nov 29, 2016

@luizirber luizirber referenced this pull request Dec 1, 2016

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Track abundance #49

6 of 7 tasks complete
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codecov-io Dec 1, 2016

Current coverage is 72.92% (diff: 58.03%)

Merging #45 into master will decrease coverage by 10.34%

@@             master        #45   diff @@
==========================================
  Files             9         11     +2   
  Lines          1106       1869   +763   
  Methods          38         38          
  Messages          0          0          
  Branches         48         48          
==========================================
+ Hits            921       1363   +442   
- Misses          167        488   +321   
  Partials         18         18          

Powered by Codecov. Last update fa02e9e...2269262

codecov-io commented Dec 1, 2016

Current coverage is 72.92% (diff: 58.03%)

Merging #45 into master will decrease coverage by 10.34%

@@             master        #45   diff @@
==========================================
  Files             9         11     +2   
  Lines          1106       1869   +763   
  Methods          38         38          
  Messages          0          0          
  Branches         48         48          
==========================================
+ Hits            921       1363   +442   
- Misses          167        488   +321   
  Partials         18         18          

Powered by Codecov. Last update fa02e9e...2269262

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Needs some tests for categorize and search, but I'm merging because we are putting too much stuff on this already!

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luizirber commented Dec 29, 2016

Needs some tests for categorize and search, but I'm merging because we are putting too much stuff on this already!

@luizirber luizirber merged commit f93f56a into master Dec 29, 2016

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@luizirber luizirber added the sbt label May 4, 2017

@luizirber luizirber deleted the sbt_search branch May 4, 2017

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