Code

Pydamage version 0.80#27

Code

Merged

maxibor merged 38 commits intomastermaxibor/pydamage:masterfrom devmaxibor/pydamage:devCopy head branch name to clipboardSep 19, 2024

+13,540-355

Commits

Commits on Jul 11, 2024

• add GtoA damage

  maxibor

  committed
  f10da15

• feat: add GtoA damage

  maxibor

  committed
  e40005d

Commits on Jul 12, 2024

• feat: add damage rescaling

  maxibor

  committed
  d3cd9cf

Commits on Jul 16, 2024

• feat: add g2a substitutions

  maxibor

  committed
  956a9b7

• feat: add rescaling feature

  maxibor

  committed
  d5ff542

• fix: damage test

  maxibor

  committed
  7b1dafe

• feat: add numba to rescale

  maxibor

  committed
  2223195

• pydamage version update

  maxibor

  committed
  b0cb6df

• dep: update conda env

  maxibor

  committed
  8670abc

• ci: update python version

  maxibor

  committed
  3344de0

• dep: remove version pinning

  maxibor

  committed
  ed5cdd0

• dep: remove python

  maxibor

  committed
  3d4e30d

• ci: update miniconda action

  maxibor

  committed
  cef0003

• ci: update rtd config

  maxibor

  committed
  f3e6895

• ci: update rtd python version

  maxibor

  committed
  d311267

• ci: update rtd dependancies

  maxibor

  committed
  3ea58d3

Commits on Jul 17, 2024

• doc: add benchmark notebook

  maxibor

  committed
  c8f0b35

• fix: grouped mode rescaling

  maxibor

  committed
  fd989b4

• doc: add rescaling notebook to rtd

  maxibor

  committed
  ec32bcb

Commits on Jul 18, 2024

• feat: add more parallelization

  maxibor

  committed
  a709509

• feat: jit cache

  maxibor

  committed
  3d5ff0d

Commits on Jul 22, 2024

• doc: update output plot

  maxibor

  committed
  d22777d

• feat: add subsample

  maxibor

  committed
  8c8d312

• feat: add pydamage CLI to bam rescaled bam output

  maxibor

  committed
  0b1b40b

Commits on Jul 23, 2024

• feat: reduce window to 13

  maxibor

  committed
  7a6deb8

• fix: remove hardcoded variable

  maxibor

  committed
  6b41c33

• feat: numpyfy code where possible

  maxibor

  committed
  e19f8b1

• Merge branch 'dev' of github.com:maxibor/pydamage into dev

  maxibor

  committed
  278efbf

• cleanup: remove old code

  maxibor

  committed
  ce1a560

• cleanup: remove comment

  maxibor

  committed
  77b0f88

• test: add subsample kwarg

  maxibor

  committed
  fd54950

• doc: (re)add repr

  maxibor

  committed
  97ba7a4

• log: add progress tracking

  maxibor

  committed
  f165c2e

Commits on Jul 24, 2024

• feat: move contig stats to dedicated modules

  maxibor

  committed
  77f0d7f

• feat: switch print to logging

  maxibor

  committed
  89c55b0

• log: add warning for no g2a used together with rescale

  maxibor

  committed
  80ba101

Commits on Jul 25, 2024

• feat: limit rescaling to window size

  maxibor

  committed
  90146a3

Commits on Sep 19, 2024

• doc: pydamage mapdamage benchmark

  maxibor

  committed
  04ec8ab