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V2.0.0 bug fixes/improvements#116

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martinghunt merged 14 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:v2.0.0_bug_fixesmartinghunt/ariba:v2.0.0_bug_fixesCopy head branch name to clipboardAug 3, 2016

+184-66

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Commits on Aug 2, 2016

• Remove % to stop argparse help breaking

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  76a6e65

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• Handle when no proper read pairs mapped

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• Typo reporting the command in versions file (had 'run' twice)

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• Bug fix when sequence names before dot have _N (N a natural number)

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• write all assemblies to a file

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Commits on Aug 3, 2016

• Fix off by one error in ref/ctg variant positions

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  d34e49e

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• Use new samtools 1.3 options. Drop Qual, as its often zero b/c assumes diploid

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  7e00fd0

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• Require samtools,bcftools v>=1.3

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  7ffed97

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• Update to use new samtools/bcftools tags

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  5612cd9

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• Round percent to 1dp

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  146d31e

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• Add plasmidfinder

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  e118dcc

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• Rename seqs from argannot for better cluster naming

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  77c3a75

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• Remove temp dir

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  24b77df

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• Version bump 2.1.0

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  3047a69

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