Code

Consecutive genes fix#148

Code

Merged

martinghunt merged 18 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:consecutive_genes_fixmartinghunt/ariba:consecutive_genes_fixCopy head branch name to clipboardNov 1, 2016

+817-17,102

Commits

Commits on Oct 20, 2016

• New class ref_seq_chooser

  

  Martin Hunt

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  0d5d8d3

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• Add ref_seq_chooser

  

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  07a608f

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• Remove dict of contigs parameter

  

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  e0b945e

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• Use new ref_seq_chooser

  

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  16b0a6f

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Commits on Oct 21, 2016

• Catch when no nucmer matches

  

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  bf758db

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• Remove debug print

  

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  c5190a2

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• More verbose logging

  

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  bb5fca9

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• Bug fix numeric sort

  

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  5c74e53

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Commits on Oct 26, 2016

• Bug fix getting wrong contig name and then key error

  

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  3d088f0

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Commits on Oct 27, 2016

• Use two overlap lengths

  

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  f86c47a

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• Write all assemblies to fasta instead of choosing one of them

  

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  173f546

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Commits on Oct 31, 2016

• Use nucmer to choose closest ref sequence

  

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  8026a0f

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• Remove dependency on mash

  

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  6fa28d0

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• Remove sspace and gapfiller

  

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  5a930ba

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Commits on Nov 1, 2016

• Use percent identity of longest match

  

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  99acc48

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• Make yes and yes_nonunique the same colour

  

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  7c54eac

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• Unhide threads option

  

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  13f2de5

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• Version bump 2.4.0

  

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  ae3b7fb

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