- changed status to closed
refactor counts/pixelmap parser names and standardize usage
Issue #21
closed
load_primer_counts()
is now the only supported way to read countsfiles, but many tools still use load_counts()
we propose to rename
load_counts()
->load_counts_legacy()
load_primer_counts()
->load_counts()
and standardize usage within lib5c
to always use the new approach
similarly, get_primermap()
should supersede get_pixelmap()
, basically by moving
get_pixelmap()
->get_pixelmap_legacy()
and making all of the following functions aliases of each other:
get_primermap()
get_pixelmap()
load_primermap()
load_pixelmap()
this is in line with the latest developments in modules2016
lib5c.tools.helpers.resolve_level()
will become mostly deprecated since only lib5c smooth
and lib5c expected
really depend on the -l/--level
flag
the pipeline will still carry around the level flag (it's never a free parameter in the pipeline context)
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major overhaul of counts/primermap parsing and plotting API
plotting API is now formalized in a new decorator:
@lib5c.util.plotting.plotter
most plotters now follow this API, except for the old heatmap plotters and cluster heatmap plotters, as well as legacy plotters
primermap/counts parsing is now standardized in line with modules2016: only two functions are supported:
load_primermap()
andload_counts()
all tools have been updated to reflect this change
lib5c.tools.helpers.resolve_level()
has been broken up intolib5c.tools.helpers.resolve_level()
andlib5c.tools.helpers.resolve_primerfile()
- this helper is only needed in a small number of toolslib5c.tools.parents.level_parser
has been broken up intolib5c.tools.parents.level_parser
andlib5c.tools.parents.primerfile_parser
-level_parser
is used rarely whileprimerfile_parser
is ubiquitousthis closes
#23, closes#21, closes#18, closes#22, closes#11, and closes#9→ <<cset f4e899afa042>>