Code

First version of the explore command#59

Code

Merged

remiolsen merged 36 commits intoNationalGenomicsInfrastructure:devNationalGenomicsInfrastructure/anglerfish:devfrom alneberg:explore_commandalneberg/anglerfish:explore_commandCopy head branch name to clipboardJan 29, 2024

+605-72

Commits

Commits on Jan 16, 2024

• Working dockerfile for arm64

  alneberg

  committed
  ff353fe

• Merged with upstream

  alneberg

  committed
  739a1be

• Add back pre-commit and prettier to conda env

  alneberg

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  f306ecd

• Ruff formatting of environment.yml

  alneberg

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  5609e0d

• Basic click interface to explore main

  alneberg

  committed
  62b57eb

Commits on Jan 17, 2024

• New AdaptorPart class and moved Adaptor to separate module

  alneberg

  committed
  eff8a9e

• Working devcontainer

  alneberg

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  25126ac

• Added click as requirement

  alneberg

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  7fa07f4

• Load adaptors function

  alneberg

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  2ee6998

• Samplesheet uses load adaptors function

  alneberg

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  fcf7238

• Explore cli outline

  alneberg

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  149312d

• Removed the unused adaptors_file argument for explore

  alneberg

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  c996de6

Commits on Jan 18, 2024

• Github actions fix, mamba environment name

  alneberg

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  8ab6ae8

• Added log file for mapping and optional B parameter

  alneberg

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  c0e3f0c

• Explore command can run minimap2

  alneberg

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  3b670c9

• Added parameter complex index to the parse_paf_lines function

  alneberg

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  28483de

• 4 threads by default for explore

  alneberg

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  5b7e9ab

• Explore command working except entropy

  alneberg

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  078a667

• Added entropy calculation and printing to the explore command

  alneberg

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  76e499a

• Change back to demux default for B in minimap2

  alneberg

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  cba68fc

Commits on Jan 22, 2024

• Fix bug in entropy calculation

  

  Johannes Alneberg

  committed
  776b146

Commits on Jan 23, 2024

• Ruff formatting for entropy file

  alneberg

  committed
  73533b5

Commits on Jan 24, 2024

• Use single multi-stage dockerfile

  alneberg

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  33c4003

Commits on Jan 25, 2024

• Fix for sneaky bug inside try except

  alneberg

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  567bf91

• Merging with upstream dev

  alneberg

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  bd84930

• Test printing histogram to csv

  alneberg

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  bfc3761

Commits on Jan 26, 2024

• Avoid zeroes in observations for entropy calculation

  alneberg

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  2319559

• Output to files instead of terminal

  alneberg

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  daed1d9

• Hopefully more unique output file names

  alneberg

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  67689bd

• Trying to fix wrong name of output files

  alneberg

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  a1321ba

• Trying out float format for entropy

  alneberg

  committed
  316b981

• Updated CLI parameters and help messages

  alneberg

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  c9dda46

• Changed back to named env in environment and specify base in dockerfile

  alneberg

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  2bbd685

• Added instructions for Arm64 installation

  alneberg

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  62aef7a

• Some note about the explore command in readme

  alneberg

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  23ef19f

Commits on Jan 29, 2024

• Fixes according to review comments

  alneberg

  committed
  5cb657e