Code

Chunked dedup#107

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Merged

agalitsyna merged 38 commits intomasteropen2c/pairtools:masterfrom chunked_dedupopen2c/pairtools:chunked_dedupCopy head branch name to clipboardApr 4, 2022

+1,334-569

Commits

Commits on Aug 25, 2021

• First try for chunked dedup

  Phlya

  committed
  657e7c6

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• Add it to main CLI function

  Phlya

  committed
  9c3362c

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• Fix bug, now tests pass

  Phlya

  committed
  ef4f63c

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Commits on Sep 6, 2021

• Add "max" mode to dedup, add readIDs to test pairs, expand tests

  Phlya

  committed
  08e4cb7

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• Update requirements

  Phlya

  committed
  39b8163

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• add scipy to test deps

  Phlya

  authored
  00c9e20

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Commits on Sep 7, 2021

• Add sklearn code

  Phlya

  committed
  99c9232

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• Three backends for deduping!

  Phlya

  committed
  7fa2d93

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• Merge branch 'chunked_dedup' of https://github.com/open2c/pairtools into chunked_dedup

  Phlya

  committed
  c6e6dc5

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• Change default to scipy

  Phlya

  committed
  d0023bd

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• Add --n-proc argument for sklearn backend

  Phlya

  committed
  7da9554

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Commits on Sep 8, 2021

• Fix bug

  Phlya

  committed
  4dc9c5c

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• Fix sum from Euclidean to Manhattan

  Phlya

  committed
  850c0d6

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Commits on Oct 17, 2021

• FIx missing stats due to dtype mismatch

  Phlya

  committed
  0d0458c

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Commits on Feb 28, 2022

• Fix for python 3.10 and fix cis_Xkb+ dtype

  Phlya

  committed
  326dacf

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Commits on Mar 2, 2022

• Chunked stats

  Phlya

  committed
  a9e8321

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• Remove trailing tabs in test data

  Phlya

  committed
  c1f8af8

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Commits on Mar 8, 2022

• Address some comments

  Phlya

  committed
  46e94ce

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Commits on Mar 9, 2022

• address more comments

  Phlya

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  f9b2fd5

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Commits on Mar 10, 2022

• Add docstring

  Phlya

  committed
  7ea80c2

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Commits on Mar 11, 2022

• Deprecate cython

  Phlya

  committed
  aff01da

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• Pass extra_cols correctly

  Phlya

  committed
  a44da0b

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Commits on Mar 17, 2022

• Add carryover parameter, default 100

  Phlya

  committed
  f990c6a

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• Docs, changes

  Phlya

  committed
  59a7284

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• Mention column order/cython deprecation in dedup

  Phlya

  committed
  1cc7781

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Commits on Mar 21, 2022

• Merge branch 'master' into chunked_dedup

  Phlya

  authored
  5d3b0c9

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Commits on Mar 23, 2022

• chunks indexing fix; refactoring of the code; dups fix; documentation of the dedp and stats from df

  agalitsyna

  committed
  2640efa

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• carryover fixed for sizes close to chunksize

  agalitsyna

  committed
  9f90351

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Commits on Mar 24, 2022

• cython version revived; parentID added to cython.

  agalitsyna

  committed
  37a4516

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Commits on Mar 28, 2022

• Fix parse "-" for stdin

  Phlya

  committed
  c518556

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Commits on Mar 29, 2022

• parents reporting checks

  agalitsyna

  committed
  29d9a9a

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• Up lowest python to 3.7

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  Phlya

  authored
  667625a

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• Up lowest python in python-package

  Phlya

  authored
  fc6c6d3

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• Require python>=3.7

  Phlya

  committed
  70660c5

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• Some formatting and minor docs changes

  Phlya

  committed
  3b18b23

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Commits on Apr 1, 2022

• Fix bug in stats!

  Phlya

  committed
  ba346b9

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Commits on Apr 4, 2022

• Add note re transitivity and backends

  Phlya

  committed
  e49477a

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• Reduce default chunksize

  Phlya

  committed
  c52f595

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