Code

Het snp bugs#139

Code

Merged

martinghunt merged 15 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:het_snp_bugsmartinghunt/ariba:het_snp_bugsCopy head branch name to clipboardSep 29, 2016

+495-397

Commits

Commits on Sep 9, 2016

• return ref,alt bases in one string

  

  Martin Hunt

  committed
  48222a6

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• remove debug prints

  

  Martin Hunt

  committed
  f753bfa

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• get ctg_nt from actual sequence; report all samtools bases and depths

  

  Martin Hunt

  committed
  7309c91

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• Rename column smtls_alt_nt to smtls_nts

  

  Martin Hunt

  committed
  3fe41a5

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• Rename column smtls_alt_depth to smtls_nts_depth

  

  Martin Hunt

  committed
  e17bd31

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• Update smtls columns and fix code/tests etc

  

  Martin Hunt

  committed
  345903d

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Commits on Sep 14, 2016

• Fix test for 23S with an indel

  

  Martin Hunt

  committed
  163421b

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• Fix multiple vars in same column by replacing , -> /

  

  Martin Hunt

  committed
  1813b1a

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• Always get het %

  

  Martin Hunt

  committed
  f388851

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• There is always a % column for snps

  

  Martin Hunt

  committed
  9d32dee

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Commits on Sep 28, 2016

• Capture het snp info

  

  Martin Hunt

  committed
  2488d98

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• Report het snps when major allele is wild type

  

  Martin Hunt

  committed
  396425d

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• Typo samtools -> bowtie2

  

  Martin Hunt

  committed
  293b8fd

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• Check output is correct

  

  Martin Hunt

  committed
  5d23712

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Commits on Sep 29, 2016

• Skip cluster if <=2 reads

  

  Martin Hunt

  committed
  b23daae

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