Consensus#23

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averagehat wants to merge 14 commits intobam-processingfrom

Commits on Jul 28, 2016

makefile for doing freebayes-based consensus on ngs_mapper output directory
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Commits on Jul 29, 2016

add consensus for freebayes
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now calls makefile correctly
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Commits on Sep 13, 2016

missing imports (samtools, ngs_mapper) also fixed
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Commits on Sep 15, 2016

fix so consensus includes reference as argument to match Makefile
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freebayes consnesus now includes sample name in filename
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consensus now accepts samplename argument to prepend to fasta IDs
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Makefile now uses consensus.py sample argument
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functionality for coverage checking
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Commits on Sep 16, 2016

consensus now considers coverage
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Commits on Oct 27, 2016

add minimum basequal parameter
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minbq now filters samtools depth call
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fixed missing minbq in cmd args doc
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Makefile now uses minbq and mind.
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