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Develop 0.3.6#19

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akikuno merged 27 commits intomainakikuno/DAJIN2:mainfrom develop-0.3.6akikuno/DAJIN2:develop-0.3.6Copy head branch name to clipboardJan 9, 2024

+726-571

Commits

Commits on Dec 24, 2023

• bump v0.3.6

  akikuno

  committed
  728d59a

• Added merge_minor_alleles to reclassify alleles with less than 10 reads.

  akikuno

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  a9399f5

• Added the function merge_minor_cluster to revert labels clustered with less than 10 reads back to the previous labels.

  akikuno

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  4bd9f7d

Commits on Dec 25, 2023

• Added a short form of installation guide to TROUBLESHOOTING.md

  akikuno

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  cefed0f

• specify python=3.10

  akikuno

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  a6bdf50

Commits on Dec 26, 2023

• Add line breaks to make the separation of the code more understandable

  akikuno

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  93c2111

• update ROADMAP

  akikuno

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  c91baab

Commits on Dec 28, 2023

• Remove the is_insertion arguments at preprocess.cache_mutation_loci because it is no longer being used.

  akikuno

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  3f66f0b

Commits on Dec 29, 2023

• move consensus.cache_mutation_loci to consensus.mutation_extractor

  akikuno

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  6b83646

• Simplyfy the error detection using cosine similarity

  akikuno

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  21c2596

• Use LocalOutlierFactor to filter abnormal control reads

  akikuno

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  94c48da

• Add consensus directory

  akikuno

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  f30fabf

• Use cosine similarity to filter dissimilar loci

  akikuno

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  c9f5aa7

• Update commit links

  akikuno

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  8b552c2

• The UCSC Blat server sometimes returns a 200 HTTP status code even when an error occurs. In such cases, "Very Early Error" is indicated in the Title. Therefore, we have made it so that it returns F…

  Show description for 4ad9c9e
  akikuno

  committed
  4ad9c9e

Commits on Jan 2, 2024

• Added preprocess.midsv_caller.convert_consecutive_indels_to_match:

  Show description for 69c56fa
  akikuno

  committed
  69c56fa

• remove underscore of the functions

  akikuno

  committed
  217355d

• Update generate_mutation_kmers to to consider indices not registered in mutation_loci as mutations by replacing them with "@". For example, if there are no mutations in mutation_loci, "=G,=C,-C" …

  Show description for 9eefaaa
  akikuno

  committed
  9eefaaa

• Change coverage_match from coverage_not_N to consider matched sequence as a coverage

  akikuno

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  e50bd57

• Update the identify_dissimilar_loci function so that it unconditionally returns True if the 'sample' shows more than 5% variation compared to the 'control'.

  akikuno

  committed
  0cbec52

• Update generate_mutation_kmers to to consider indices not registered in mutation_loci as mutations by replacing them with "@". For example, if there are no mutations in mutation_loci, "=G,=C,-C" …

  Show description for 5b16f1a
  akikuno

  committed
  5b16f1a

Commits on Jan 5, 2024

• rename function of cssplit_to_base from cstag_to_base

  akikuno

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  71d4303

• fix the function name of fetch_seq_coordinates

  akikuno

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  a57862b

• Add allele_merger.py to merge minor alleles

  akikuno

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  b075296

• update ROADMAP.md

  akikuno

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  a704118

Commits on Jan 7, 2024

• Add is_consensus argument: When it comes to consensus, if the difference between sample and control is more than 20%, it is unconditionally considered a mutation.

  akikuno

  committed
  7bca459

• update commit log

  akikuno

  committed
  40588a1