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Commits on Jan 16, 2025

• Updates to v1.4.1

  

  Samuel Horsfield

  committed
  fe30b1a

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• Corrects size_t error with GFF coordinates

  

  Samuel Horsfield

  committed
  5ad7473

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Commits on Jan 14, 2025

• Corrects issue with GFF start indexing

  

  Samuel Horsfield

  committed
  e37ce7a

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• Corrects GFF indexing error

  

  Samuel Horsfield

  committed
  c6b3aa1

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Commits on Dec 18, 2024

• Updates docs and test with new --gene-finding-only option

  

  Samuel Horsfield

  committed
  59d32b3

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• Adds direct GFF writing

  samhorsfield96

  committed
  665c42e

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Commits on Oct 29, 2024

• Fixes saving of fmindex temp files

  

  Samuel Horsfield

  committed
  464e61e

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• Fixes saving of fmindex temp files

  

  Samuel Horsfield

  committed
  ca044bd

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• Corrects fm index read error

  

  Samuel Horsfield

  committed
  cf449ea

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Commits on Oct 25, 2024

• Sets num_bytes to 1 for fmindexing

  

  Samuel Horsfield

  committed
  077b7b7

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• Corrects fm indexing using file instead of in memory

  

  Samuel Horsfield

  committed
  c1c06dc

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• Updates sdsl to use decimal parsing to handle longer strings

  samhorsfield96

  committed
  d7acc5c

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• Fixes Keyerror during refinding

  samhorsfield96

  committed
  4ad6cd4

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Commits on Oct 18, 2024

• Resolved all conflicts by accepting incoming changes

  samhorsfield96

  committed
  0430b35

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• Implements all changes for merging into master

  samhorsfield96

  committed
  5cb6416

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• Corrects issue with writing refound genes for alignment

  samhorsfield96

  committed
  629d5d2

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• Fixes issue with clusters being incorrect

  samhorsfield96

  committed
  4a4a8a4

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• Removes debugging files

  samhorsfield96

  committed
  415c0aa

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• Deals with issue with paralog clusters having centroid sequence not in cluster itself

  samhorsfield96

  committed
  f0627a1

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• Corrects OOR issue where no genes removed from colour

  samhorsfield96

  committed
  da08d32

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Commits on Oct 17, 2024

• Updates tests and docs

  samhorsfield96

  committed
  644644f

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• Updates tests and docs

  samhorsfield96

  committed
  2207013

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• Corrects issue with node ID remapping

  samhorsfield96

  committed
  b37653a

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• Corrects querying of genes

  samhorsfield96

  committed
  7f2c05b

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• Updates saving of output files for querying

  samhorsfield96

  committed
  b91fc7d

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Commits on Oct 14, 2024

• Corrects issue with alignment of refound genes

  samhorsfield96

  committed
  12983c9

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• Corrects issue with writing protein sequence

  samhorsfield96

  committed
  558cff8

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• Corrects issue with get_core_gene_nodes dict iteration

  samhorsfield96

  committed
  2f32cec

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• Corrects issue with get_core_gene_nodes dict iteration

  samhorsfield96

  committed
  18b4909

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• Enables saving of FM indexes in output directory, not where original FASTAs are

  samhorsfield96

  committed
  dcd0465

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• Corrects issue with small core genome

  samhorsfield96

  committed
  1ac83f8

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• Removes defaults channel from macOS environment

  samhorsfield96

  committed
  2be700b

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• Removes defaults channel

  samhorsfield96

  committed
  6f5068f

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• Ensure centroids also included in ORFs_to_remove

  samhorsfield96

  committed
  c916182

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Commits on Oct 12, 2024

• Corrects issue with genes with 0 id being incorrectly indexed

  samhorsfield96

  committed
  59fb0c0

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