cli_update-pull_request#1

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tmfarrell wants to merge 17 commits intolerch-a:masterfrom

tmfarrell:master

Commits on Apr 4, 2018

updated createFinalHaplotypeTable
Tim Farrell
committed

Commits on Apr 13, 2018

allow for using previously computed data
Tim Farrell
committed
contingency table read/melt fix
Tim Farrell
committed

Commits on Apr 20, 2018

add saving intermediate steps to RDS
Tim Farrell
committed

Commits on Apr 24, 2018

allow different fwd/rev read sizes for each amplicon
Tim Farrell
committed
updated README
Tim Farrell
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updated README
Tim Farrell
committed

Commits on May 9, 2018

allow differing indel thresholds for each amplicon
Tim Farrell
committed
updated README: cmd-line usage
Tim Farrell
committed

Commits on Jun 1, 2018

updated cmd-line usage
Tim Farrell
committed

Commits on Jul 17, 2018

update readme
Tim Farrell
committed

Commits on Jul 24, 2018

add return_full_haplotypes flag
Tim Farrell
committed

Commits on Aug 16, 2018

bug fixes
Tim Farrell
committed
updated readme
Tim Farrell
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updated readme
Tim Farrell
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remove sourcing local files
Tim Farrell
committed

Commits on Oct 9, 2018

comments for callHaplotype fcn ; misc updates
Tim Farrell
committed