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@scottcain
Created October 24, 2011 13:58
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broken sam semantic track
[main:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir '/Library/WebServer/Documents/gbrowse2/databases/volvox'
[samdb:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /Library/WebServer/Documents/gbrowse2/databases/volvox/volvox.fa
-bam /Library/WebServer/Documents/gbrowse2/databases/volvox/volvox.sort.bam
search options = none
[TRACK DEFAULTS]
glyph = generic
height = 10
bgcolor = lightgrey
fgcolor = black
font2color = blue
label density = 25
bump density = 100
database = main
# where to link to when user clicks in detailed view
link = AUTO
[Alignments]
feature = match
glyph = segments
key = Example alignments
[Alignments:10000]
glyph = box
label = 0
[Alignments:45000]
glyph = box
bump = 0
label = 0
[Reads]
feature = match
glyph = segments
draw_target = 1
show_mismatch = 1
mismatch_color = red
database = samdb
bgcolor = blue
height = 5
label density = 50
bump = fast
key = Reads
category = Reads
[Reads:5000]
feature = coverage
glyph = wiggle_density
database = samdb
height = 20
bicolor_pivot = 90
pos_color = blue
neg_color = red
label = 0
draw_target = 0
show_mismatch = 0
bump = 0
[CoverageDensity]
feature = coverage
glyph = wiggle_density
database = samdb
height = 20
bicolor_pivot = 90
pos_color = blue
neg_color = red
key = Coverage (density)
category = Reads
label = 0
[Pairs]
feature = read_pair
glyph = segments
draw_target = 1
show_mismatch = 1
mismatch_color = red
database = samdb
bgcolor = violet
height = 5
label density = 50
bump = fast
key = Read pairs
category = Reads
[Pairs:2000]
feature = coverage
glyph = wiggle_density
database = samdb
height = 20
bicolor_pivot = 90
pos_color = purple
neg_color = red
label = 0
draw_target = 0
show_mismatch = 0
bump = 0
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