Bam processing (WIP)#19

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averagehat wants to merge 45 commits intodevfrom

Commits on Feb 10, 2016

added tagreads (tags all reads, doesn't skip any)
averagehat
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Commits on Feb 12, 2016

added new implementation of consensus
averagehat
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Commits on Feb 22, 2016

update
averagehat
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Commits on Feb 23, 2016

consensus now handles multiple alts
averagehat
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Commits on Feb 24, 2016

various fixes
Panciera
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refactoring to simplify and remove deprecated funcs
Panciera
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Commits on Feb 27, 2016

added tests,refactored vcf dict flattening
Panciera
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Commits on Mar 2, 2016

add missing dependencies
Panciera
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fixed ordering bug
Panciera
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fixed groupby bug
Panciera
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fixed make_consensus
Panciera
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more tests
Panciera
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add failing test
Panciera
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Commits on Mar 3, 2016

Commits on Mar 4, 2016

Commits on Mar 22, 2016

Merge branch 'bam-processing' of https://github.com/VDBWRAIR/bioframework into bam-processing
Panciera
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fix VCFRow instantiation
Panciera
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Commits on Mar 23, 2016

more info in consensus's stuff
Panciera
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add doc for low-depth handling
Panciera
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restore lowdepth->N so tests can maybe pass
Panciera
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fixed duplcate args error
Panciera
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Commits on Apr 17, 2017

ignroe
Panciera
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