new snp1 load feat-file=./eg2.raw.vcf,feat-file-type=VCF

# expand SNP loci by a factor of 100X
new ssl1 scaled-segment-list feat-track=snp1,scale=100

# highlight SNP loci
new hssl1 rectangle feat-track=snp1,opacity=0.2,innerf=0.32,outerf=1.15,color1=#909090,color2=black

# print location of SNP loci
new sll label feat-track=snp1,innerf=1.155,outerf=1.17,label-function=position,label-type=spoke,packer=none

# percent GC plot
%GC0-100 innerf=1.03,opacity=0.6,heightf=0.07,graph-min=0,graph-max=100,window-size=100

# forward and reverse strand genes
small-cgap
genes-fwd heightf=0.05
tRNAs-fwd heightf=0.05,innerf=same
rRNAs-fwd heightf=0.05,innerf=same
tiny-cgap
genes-rev heightf=0.05
tRNAs-rev heightf=0.05,innerf=same
rRNAs-rev heightf=0.05,innerf=same

small-cgap

# reference base(s)
new snp rectangle heightf=0.1,feat-track=snp1,color1=black,color2=black
new snprb label heightf=0.05,innerf=same+0.005,label-function=snp_ref_base,feat-track=snp1,packer=none,text-color=white,label-type=spoke,font-height-frac=0.3
small-cgap heightf=0.01
medium-label label-text=Reference Base(s)
small-cgap

# all variants
new all_snps rectangle feat-type=SNP,heightf=0.1,color1=black,color2=black
# variant base(s)
new all_snpsl label heightf=0.05,innerf=same+0.005,label-function=snp_base,feat-type=SNP,packer=none,text-color=white,snp-query=../coverage_plots/eg2.sorted.bam,label-type=spoke,font-height-frac=0.3

medium-label label-text=All Variants

# connect outer scaled circle to inner unscaled circle
new hssl2 rectangle innerf=0.22,outerf=0.32,feat-track=ssl1,opacity=0.2,color1=#909090,color2=black,stroke-width=1,inner-scale=none,outer-scale=default

# restore unscaled coordinates
new SSLR scaled-segment-list scale=1,feat-type=dummy

# inner (unscaled) circle
coords innerf=0.22,heightf=0.006,tick-interval=1000,label-interval=10000,label-units=kb

tiny-cgap

new snp2 rectangle heightf=0.02,feat-track=snp1,color1=black,color2=black

tiny-cgap

# forward and reverse strand genes
genes-fwd heightf=0.02
tRNAs-fwd innerf=same,outerf=same
rRNAs-fwd innerf=same,outerf=same
tiny-cgap
genes-rev heightf=0.02
tRNAs-rev innerf=same,outerf=same
rRNAs-rev innerf=same,outerf=same
tiny-cgap