Report full codons and original sequence names#145

Merged

martinghunt merged 13 commits intosanger-pathogens:masterfrom martinghunt:report_full_codons

Oct 6, 2016

+454-372

Commits on Oct 5, 2016

Report complete codons for amino acid changes
Martin Hunt
committed
remove commented out code
Martin Hunt
committed
Add option rename_file
Martin Hunt
committed
Check if rename file exists
Martin Hunt
committed
Remove warning message
Martin Hunt
committed
Add column with original ref seq name
Martin Hunt
committed
Add new ariba_ref_name column to report
Martin Hunt
committed
Remove unused variable
Martin Hunt
committed
Rename report.all file to discourage user from looking at it
Martin Hunt
committed
Remove reportfilter command
Martin Hunt
committed
Fix tests by adding new ariba_ref_name column to report
Martin Hunt
committed
Spelling typo
Martin Hunt
committed
Add complete codons to test report files
Martin Hunt
committed