[data]
# directory where BAM files are
bam_prefix = ./test-data/bam-data/
# directory where MISO output is
miso_prefix = ./test-data/miso-data/

bam_files = [
    "heartWT1.sorted.bam",
    "heartWT2.sorted.bam",
    "heartKOa.sorted.bam",
    "heartKOb.sorted.bam"]

miso_files = [
    "heartWT1",
    "heartWT2",
    "heartKOa",
    "heartKOb"]

[plotting]
# Dimensions of figure to be plotted (in inches)
fig_width = 7
fig_height = 5 
# Factor to scale down introns and exons by
intron_scale = 30
exon_scale = 4
# Whether to use a log scale or not when plotting
logged = False 
font_size = 6

bar_posteriors = False

# Max y-axis
ymax = 150

# Axis tick marks
nyticks = 3
nxticks = 4

# Whether to show axis labels
show_ylabel = True
show_xlabel = True

# Whether to plot posterior distributions inferred by MISO
show_posteriors = True 

# Whether to plot the number of reads in each junction
number_junctions = True

resolution = .5
posterior_bins = 40
gene_posterior_ratio = 5

# List of colors for read denisites of each sample
colors = [
    "#CC0011",
    "#CC0011",
    "#FF8800",
    "#FF8800"]

# Number of mapped reads in each sample
# (Used to normalize the read density for RPKM calculation)
coverages = [
    6830944,
    14039751,
    4449737, 
    6720151]

# Bar color for Bayes factor distribution
# plots (--plot-bf-dist)
# Paint them blue
bar_color = "b"

# Bayes factors thresholds to use for --plot-bf-dist
bf_thresholds = [0, 1, 2, 5, 10, 20]

##
## Names of colors for plotting
##
# "b" for blue
# "k" for black
# "r" for red
# "g" for green
#
# Hex colors are accepted too.