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'Finish line' fixes towards ENA validity #43

Merged
merged 8 commits into from
Jan 20, 2016
Merged

'Finish line' fixes towards ENA validity #43

merged 8 commits into from
Jan 20, 2016

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satta
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@satta satta commented Jan 15, 2016

  • strip leading/trailing [Nn]s
  • drop genes w/o CDS
  • do not cut off partial codons but fill them up with Ns to be translated
  • add /codon_start qualifier
  • do not discard some gaps

Also:

  • dead code cleanup
  • make ABACAS parameters configurable

aslett1 added a commit that referenced this pull request Jan 20, 2016
@aslett1
Merge pull request #43 from satta/work
0ca08b5 
'Finish line' fixes towards ENA validity
@aslett1 aslett1 merged commit 0ca08b5 into sanger-pathogens:master Jan 20, 2016
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@satta @aslett1