The config file contains the default options for running bulkVis. There are
three sections: data, plot_opts, and labels. A config file can either
be generated by set_config.py with a bulk-fast5 file
to determine what labels are available or by editing the sample config file
that is provided in this repository.
[data] describes the directories used by bulkVis
| Option | Type | Description |
|---|---|---|
data |
string | Path to the bulk-fast5 file directory |
out |
string | Path to where read files will be written, this path must exist |
map |
string | Path to where map files directory (created by gen_bmf.py) |
[plot_opts] describes default options for the squiggle plot
| Option | Type | Description |
|---|---|---|
wdg_width |
int | The width of the left-hand panel in bulkVis |
plot_width |
int | The width of the squiggle plot in pixels |
plot_height |
int | The height of the squiggle plot in pixels |
y_min |
int | The minimum value of the y-axis, when this axis is fixed |
y_max |
int | The maximum value of the y-axis, when this axis is fixed |
label_height |
int | The height, on the y-axis, where labels will be rendered |
upper_cut_off |
int | The maximum value that will be plot |
lower_cut_off |
int | The minimum value that will be plot |
output_backend |
string | This determines how the plot is rendered in the browser; must be one of canvas, svg, webgl |
[labels] describes the labels that should be shown by default and which 'jump-to'
options are available these are derived from bulk-fast5 files, specifically the
IntermediateData and StateData groups. If a classification is not found in a file
it will not be added as an option in the gui. The script set_config.py
can be used to populate the entire config file and add in labels.
[data]
dir = /path/to/bulkfile/directory
out = /path/to/readfile/directory
map = /path/to/mapfile/directory
[plot_opts]
wdg_width = 300
plot_width = 1600
plot_height = 1000
y_min = 0
y_max = 2200
label_height = 800
upper_cut_off = 2200
lower_cut_off = -1000
; recommended that this is kept as 'canvas' opts: ['canvas', 'svg', 'webgl']
output_backend = canvas
[labels]
adapter = True
mux_uncertain = True
strand1 = False
user1 = True
event = False
user2 = False
multiple = False
unclassed = False
pore = True
strand = True
transition = True
unavailable = False
zero = False
saturated = False
unblocking = True
good_single = False
below = False
above = True
inrange = False
unclassified = False
unclassified_following_reset = False
pending_manual_reset = False
pending_mux_change = False