Code

Torsten issues#146

Code

Merged

martinghunt merged 16 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:torsten_issuesmartinghunt/ariba:torsten_issuesCopy head branch name to clipboardOct 12, 2016

+4,215-96

Commits

Commits on Oct 6, 2016

• Try to use when appropriate

  

  Martin Hunt

  committed
  914c5a3

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• Add debug option

  

  Martin Hunt

  committed
  470d054

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• Add --force option

  

  Martin Hunt

  committed
  cb7ef0e

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• Unique option group names

  

  Martin Hunt

  committed
  1c06dfc

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• new method _has_any_part_of_ref_assembled

  

  Martin Hunt

  committed
  fba4903

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Commits on Oct 7, 2016

• Fix coverage column to have 3 values

  

  Martin Hunt

  committed
  7c21590

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• Add partial as an option for assembled column

  

  Martin Hunt

  committed
  7049412

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• Run mash sketch on fasta of all ref seqs

  

  Martin Hunt

  committed
  6eef738

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• Run mash against all ref seqs, not just the cluster refs

  

  Martin Hunt

  committed
  48c3c79

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Commits on Oct 10, 2016

• Print stack trace if reporting fails

  

  Martin Hunt

  committed
  340f89f

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• Bug fix for synonymous variants

  

  Martin Hunt

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  f30f850

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Commits on Oct 11, 2016

• Bug fix handling multiple vars in one codon

  

  Martin Hunt

  committed
  6730650

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• Handle inserted or deleted codon

  

  Martin Hunt

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  86f5995

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Commits on Oct 12, 2016

• Add mash sketch file

  

  Martin Hunt

  committed
  332c71f

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• Check mash sketch file is present

  

  Martin Hunt

  committed
  d3acd0c

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• Version bump 2.3.0

  

  Martin Hunt

  committed
  ebd2baa

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