Code

pairtools 1.0.0 updates#117

Code

Merged

agalitsyna merged 52 commits intomasteropen2c/pairtools:masterfrom pre0.4.0open2c/pairtools:pre0.4.0Copy head branch name to clipboardJun 1, 2022

+13,736-6,264

Commits

Commits on Apr 7, 2022

• restrict fixes

  Show description for 5a1cc76
  agalitsyna

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  5a1cc76

• pairtools flip fix for unannotated chromosomes, resolving #91

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  7480fb5

Commits on Apr 8, 2022

• merge improvements, header merge fixed

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  agalitsyna

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  31d22f7

• merge improvements

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  4feda3a

• I/O improvement

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  b002dbe

Commits on Apr 11, 2022

• Parse2 update (#99) (#109)

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  agalitsyna

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  db465f6

• black

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  fed4699

Commits on Apr 12, 2022

• separate cli and lib

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  5d5a5bc

• Merge pairlib into pairtools.lib.

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• scalings bugfix

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  1a8469b

Commits on Apr 14, 2022

• CLI for scalings added.

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• scaling tests

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• pairtools stats chromosome sizes

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• stats output in yaml format

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• yaml dependency added to the workflows

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• requirement update

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• Python 3.10 added to workflow

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• Python 3.10 fix

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• Header CLI (#121)

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  agalitsyna

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  cdee78d

• pairtools phase critical update (#114)

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  agalitsyna

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  8a8a9fb

• Removed python 3.10 testing becuase of glibc problem in conda

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  1bd71e6

• phase unmapped chrom fix

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  edfa4f3

Commits on Apr 16, 2022

• add_cols fix for lib.parse

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Commits on Apr 19, 2022

• additional columns fix

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• logger added

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• junction index update and parsing docs fix

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• Example walkthrough added.

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• example cleanup

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Commits on Apr 20, 2022

• minor change

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  08fd8e6

Commits on Apr 25, 2022

• imporant fixes: - cython dedup with no-parent id forgotten counter reset; - sphinx doc update (added pysam); - header warning if empty and error if try to add a field to empy one

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  9c26b51

Commits on Apr 26, 2022

• phasing fix of the phase2 bug

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• walkthrough on phasing. improved walkthrough on parse

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• headerops get_colnames and viewframe input validation for scalings added.

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• scalings docstrings

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• bioframe dependency added

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Commits on Apr 27, 2022

• Add summaries (#105)

  Show description for 2bdac9a
  

  Phlya

  and

  agalitsyna

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• PairCounter merge fix

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• stats forgotten _fileio fix

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• R1/2 substituted with R1-2; docs improved

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Commits on May 3, 2022

• Benchmarks added

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Commits on May 4, 2022

• Extract tile info much faster (pd.str.split sucks)

  Phlya

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• snakefile and restriction walkthrough update.

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Commits on May 11, 2022

• Benchmarks finalization

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  faf5878

• benchmark fixes

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Commits on May 19, 2022

• Fir dtype so it gets saved

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Commits on May 20, 2022

• [WIP] Stats split by filters (#132)

  Show description for 9a21e15
  

  Phlya

  and

  agalitsyna

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  9a21e15

• Fix bug in complexity estimation

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  dabf4b7

• Add yaml2pandas function

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  b08e8cd

• Make by tile dups int

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Commits on May 31, 2022

• Markasdup lib removed; markasdup CLI explanation improved

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  7647057

Commits on Jun 1, 2022

• dedup filter stats added and tested

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• Black

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