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‎README.md

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@@ -60,7 +60,7 @@ cat example/work.sh
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```
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![gene cluster image](example/out3.notitle.png)
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<br><br><br>
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![gene cluster image](example/out2.notitle.png)
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![gene cluster image](example/out2.notitle.svg)
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<br><br><br>
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![gene cluster image](example/out1.notitle.png)
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<br><br><br>

‎data/NC_017659.1.indel.fa.longreads.map2ref.sort.bam.bai

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‎example/feature.color.label.conf.out2

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‎example/feature.crossing.link.out2

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@@ -5750,3 +5750,39 @@ NC_017659.1.fake_6242_5898_1_0_0_0_6:2:1_2:2:5_258d.NC_017659.1.1700.5900.read2.
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NC_017659.1.fake_6242_5898_1_0_0_0_6:2:1_2:2:5_258d.NC_017659.1.1700.5900.read2.cr.-1.155forward.-1.1 NC_017659.1.fake_6242_5898_1_0_0_0_6:2:1_2:2:5_258d.NC_017659.1.1700.5900.read2.mate.cr.-1.0fake.-1.1 cross_link_shape line
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NC_017659.1.fake_6242_5898_1_0_0_0_6:2:1_2:2:5_258d.NC_017659.1.1700.5900.read2.cr.-1.155forward.-1.1 NC_017659.1.fake_6242_5898_1_0_0_0_6:2:1_2:2:5_258d.NC_017659.1.1700.5900.read2.mate.cr.-1.0fake.-1.1 cross_link_order 0
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NC_017659.1.fake_6242_5898_1_0_0_0_6:2:1_2:2:5_258d.NC_017659.1.1700.5900.read2.cr.-1.155forward.-1.1 NC_017659.1.fake_6242_5898_1_0_0_0_6:2:1_2:2:5_258d.NC_017659.1.1700.5900.read2.mate.cr.-1.0fake.-1.1 feature_popup_title NC_017659.1 -> 5898:5900:47M3D105M : 5900:5900:null
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ cross_link_shape quadrilateral
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ cross_link_anchor_pos low_up
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ cross_link_color orange
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ cross_link_opacity 0.5
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ cross_link_shift_y +3:-3
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ crosslink_stroke_style stroke:black;stroke-width:0.2;
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ feature_popup_title query -> NC_017659.1.fake:5460:147060;target -> NC_017659.1:5460:147060;strand -> +;indentity -> 100.00%;coverage -> query:100%;target:100%
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ cross_link_order 0.25
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pO83_CORR.indel.NC_017659.1.fake.5460.147060.1.+ pO83_CORR.NC_017659.1.5460.147060.1.+ edge_coordinate_feature_out_of_list pO83_CORR.indel,NC_017659.1.fake,1700:6000 ->pO83_CORR,NC_017659.1,1700:5900 -> pO83_CORR.indel,NC_017659.1.fake,6000 -> pO83_CORR,NC_017659.1,5900
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ cross_link_shape quadrilateral
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ cross_link_anchor_pos low_up
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ cross_link_color orange
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ cross_link_opacity 0.4997
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ cross_link_shift_y +3:-3
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ crosslink_stroke_style stroke:black;stroke-width:0.2;
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ feature_popup_title query -> NC_017659.1.fake:1891:5257;target -> NC_017659.1:2101:5468;strand -> +;indentity -> 99.94%;coverage -> query:99.9703087885986%;target:100%
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ cross_link_order 0.5
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pO83_CORR.indel.NC_017659.1.fake.1891.5257.1.+ pO83_CORR.NC_017659.1.2101.5468.1.+ edge_coordinate_feature_out_of_list 0
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ cross_link_shape quadrilateral
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ cross_link_anchor_pos low_up
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ cross_link_color orange
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ cross_link_opacity 0.49945
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ cross_link_shift_y +3:-3
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ crosslink_stroke_style stroke:black;stroke-width:0.2;
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ feature_popup_title query -> NC_017659.1.fake:1:1898;target -> NC_017659.1:1:1898;strand -> +;indentity -> 99.89%;coverage -> query:100%;target:100%
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ cross_link_order 0.75
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pO83_CORR.indel.NC_017659.1.fake.1.1898.1.+ pO83_CORR.NC_017659.1.1.1898.1.+ edge_coordinate_feature_out_of_list pO83_CORR.indel,NC_017659.1.fake,1700:6000 ->pO83_CORR,NC_017659.1,1700:5900 -> pO83_CORR.indel,NC_017659.1.fake,1700 -> pO83_CORR,NC_017659.1,1700
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ cross_link_shape quadrilateral
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ cross_link_anchor_pos low_up
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ cross_link_color orange
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ cross_link_opacity 0.5
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ cross_link_shift_y +3:-3
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ crosslink_stroke_style stroke:black;stroke-width:0.2;
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ feature_popup_title query -> NC_017659.1.fake:5251:5460;target -> NC_017659.1:1891:2100;strand -> +;indentity -> 100.00%;coverage -> query:100%;target:100%
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ cross_link_order 1
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pO83_CORR.indel.NC_017659.1.fake.5251.5460.1.+ pO83_CORR.NC_017659.1.1891.2100.1.+ edge_coordinate_feature_out_of_list 0

‎example/main.2.conf

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@@ -7,9 +7,13 @@ reads_mapping=short_reads,1,pO83_CORR,NC_017659.1,0,../data/NC_017659.1.indel.fa
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reads_mapping=long_reads,1,pO83_CORR,NC_017659.1,0,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.longreads.sort.bam:../data/NC_017659.1.fa,stack,70->100,0,20->30->2,ytick_label_text,hgrid_flag,green:black,1:1,2:6:0.2:0,15:15,0:10:40 color_height_cs->M:green:opacity0.8:height0.5:1bp:rect,I:red:opacity1:height0.9:6bp:rect,D:black:opacity1:height0.8:3bp:rect,N:blue:opacity1:height0.2:1bp:rect,S:blue:opacity0.6:height0.4:10bp:rect,H:blue:opacity0.6:height0.2:10bp:rect,P:blue:opacity1:height0.2:1bp:rect,X:Purple:opacity1:height0.6:1bp:rect,reverse:#1E90FF:opacity0.6:height0.8:6bp:arrow,forward:green:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
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reads_mapping=long_reads,1,pO83_CORR.indel,NC_017659.1.fake,0,../data/NC_017659.1.indel.fa.longreads.map2ref.sort.bam:../data/NC_017659.1.indel.fa,stack,-20->-100,0,20->30->2,ytick_label_text,hgrid_flag,green:black,1:1,2:6:0.2:0,15:15,0:10:40 color_height_cs->M:green:opacity0.8:height0.5:1bp:rect,I:red:opacity1:height0.9:6bp:rect,D:black:opacity1:height0.8:3bp:rect,N:blue:opacity1:height0.2:1bp:rect,S:blue:opacity0.6:height0.4:10bp:rect,H:blue:opacity0.6:height0.2:10bp:rect,P:blue:opacity1:height0.2:1bp:rect,X:Purple:opacity1:height0.6:1bp:rect,reverse:#1E90FF:opacity0.6:height0.8:6bp:arrow,forward:green:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
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tracks_shift_y=pO83_CORR,0,+1:-0
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#synteny = order->0->1,query->pO83_CORR.indel:target->pO83_CORR,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.blast.m6,blast_m8,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3,sort->1
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synteny = order->0->1,query->pO83_CORR.indel->NC_017659.1.fake:target->pO83_CORR->NC_017659.1,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.blast.m6,blast_m8,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3,sort->1
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allow_feature_out_of_list=synteny
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display_segment_name=yes,center,shift_y:+2,fontsize:10,color:black,order:5 # yes or no , for scaffold name
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‎example/main.2.conf.out2

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feature_label_order = 4
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feature_label_size = 10
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scale_ratio = 1700
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synteny = order->0->1,query->pO83_CORR.indel->NC_017659.1.fake:target->pO83_CORR->NC_017659.1,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.blast.m6,blast_m8,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3,sort->1
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legend_stroke_width = 0.5
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scale_display = yes
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scale_color = green
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legend_height_space = 0.1
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legend_width_margin = 0.15
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feature_shift_x = 0
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feature_keywords = xx,long_reads,short_reads,ylabel
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feature_keywords = xx,long_reads,short_reads,synteny,ylabel
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track_style = fill:blue;opacity:0.2
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feature_x_extent = 0bp,0bp
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label_rotate_angle = 0
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feature_color = rgb(50,205,50)
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scale_position = low
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feature_border_size = 0
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display_segment_name = no,center,shift_y:+1,fontsize:10,color:black,order:5
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feature_shape = arrow
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display_segment_name = yes,center,shift_y:+2,fontsize:10,color:black,order:5
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legend_font_size = 20
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legend_height_percent = 0.2
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track_order = 1
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distance_closed_feature = 200
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scale_width = 0.5
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color_sample_name_default = green
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tracks_shift_y = pO83_CORR,0,+1:-0
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allow_feature_out_of_list = synteny
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scale_tick_padding_y = 10
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absolute_postion_in_title = yes
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pos_feature_label = right_low
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reads_mapping = short_reads,1,pO83_CORR,NC_017659.1,0,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam:../data/NC_017659.1.fa,paired:color->Orange:opacity->1:cross_link_height_line->0.2,5->30,0,10->30->3,ytick_label_text,0,green:black,1:1,2:6:0.2:0.1,15:15,10:10:40 ylabel->illuminate pair-end read mapping,gap:50bp,fontsize:13,color:black
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reads_mapping = short_reads,1,pO83_CORR,NC_017659.1,0,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam:../data/NC_017659.1.fa,stack,35->65,0,10->40->3,ytick_label_text,0,green:black,1:1,2:6:0.2:0.1,15:15,10:10:40 ylabel->illuminate pair-end read mapping stack,gap:50bp,fontsize:13,color:black
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reads_mapping = long_reads,1,pO83_CORR,NC_017659.1,0,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.longreads.sort.bam:../data/NC_017659.1.fa,stack,70->100,0,20->30->2,ytick_label_text,hgrid_flag,green:black,1:1,2:6:0.2:0,15:15,0:10:40 color_height_cs->M:green:opacity0.8:height0.5:1bp:rect,I:red:opacity1:height0.9:6bp:rect,D:black:opacity1:height0.8:3bp:rect,N:blue:opacity1:height0.2:1bp:rect,S:blue:opacity0.6:height0.4:10bp:rect,H:blue:opacity0.6:height0.2:10bp:rect,P:blue:opacity1:height0.2:1bp:rect,X:Purple:opacity1:height0.6:1bp:rect,reverse:#1E90FF:opacity0.6:height0.8:6bp:arrow,forward:green:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
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reads_mapping = long_reads,1,pO83_CORR.indel,NC_017659.1.fake,0,../data/NC_017659.1.indel.fa.longreads.map2ref.sort.bam:../data/NC_017659.1.indel.fa,stack,-20->-100,0,20->30->2,ytick_label_text,hgrid_flag,green:black,1:1,2:6:0.2:0,15:15,0:10:40 color_height_cs->M:green:opacity0.8:height0.5:1bp:rect,I:red:opacity1:height0.9:6bp:rect,D:black:opacity1:height0.8:3bp:rect,N:blue:opacity1:height0.2:1bp:rect,S:blue:opacity0.6:height0.4:10bp:rect,H:blue:opacity0.6:height0.2:10bp:rect,P:blue:opacity1:height0.2:1bp:rect,X:Purple:opacity1:height0.6:1bp:rect,reverse:#1E90FF:opacity0.6:height0.8:6bp:arrow,forward:green:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
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label_text_alignment_baseline = baseline
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scale_order = -1

‎example/main.3.conf

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###############################----This Is wanted, 如果要画read mapping下面参数是必须的----##############################
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## long reads mapping
5-
reads_mapping=long_reads,1,chr14,14,0,../data/pacbio.chr14.sort.bam:../data/chr14.fa,stack,-10->-110,0,20->30->2,ytick_label_text,hgrid_flag,green:black,1:1,2:6:0.2:0,15:15,0:10:40 color_height_cs->M:green:opacity0.8:height0.5:1bp:rect,I:red:opacity1:height0.9:6bp:rect,D:black:opacity1:height0.8:3bp:rect,N:blue:opacity1:height0.2:1bp:rect,S:blue:opacity0.6:height0.4:10bp:rect,H:blue:opacity0.6:height0.2:10bp:rect,P:blue:opacity1:height0.2:1bp:rect,X:Purple:opacity1:height0.6:1bp:rect,reverse:#1E90FF:opacity0.6:height0.8:6bp:arrow,forward:green:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect ylabel->pacbio read mapping stack,gap:150bp,fontsize:13,color:black
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reads_mapping=long_reads,1,chr14,134,0,../data/pacbio.chr14.sort.bam:../data/chr14.fa,stack,-10->-110,0,20->30->2,ytick_label_text,hgrid_flag,green:black,1:1,2:6:0.2:0,15:15,0:10:40 color_height_cs->M:green:opacity0.8:height0.5:1bp:rect,I:red:opacity1:height0.9:6bp:rect,D:black:opacity1:height0.8:3bp:rect,N:blue:opacity1:height0.2:1bp:rect,S:blue:opacity0.6:height0.4:10bp:rect,H:blue:opacity0.6:height0.2:10bp:rect,P:blue:opacity1:height0.2:1bp:rect,X:Purple:opacity1:height0.6:1bp:rect,reverse:#1E90FF:opacity0.6:height0.8:6bp:arrow,forward:green:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect ylabel->pacbio read mapping stack,gap:150bp,fontsize:13,color:black
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## short pair-end reads mapping as pair

‎example/note.txt

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共线性切分问题：
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假设上下一共4个点的坐标已知，同时region左右边缘的坐标也已知，这样就可以计算出region左右边上被切分的点的坐标。只要比对文件中的的pair和region有overlap就保留。
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但是有的pair中的上方或下方超出list中region的区域了，这样如何得到上面或者下方的pair的坐标呢？
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‎example/out2.cat.log

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@@ -8,20 +8,50 @@ set -vex;cat out2.pO83_CORR.NC_017659.1.1.1.short_reads.ylabel.setting.conf out2
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set -vex;cat out2.pO83_CORR.NC_017659.1.1.1.1700.5900.mapping.crosslink.conf >out2.pO83_CORR.out2.reads_mapping.crosslink;rm out2.pO83_CORR.NC_017659.1.1.1.1700.5900.mapping.crosslink.conf;echo output out2.pO83_CORR.out2.reads_mapping.crosslink
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set -vex;cat out2.pO83_CORR.indel.NC_017659.1.fake.1.4.long_reads.ylabel.gff out2.pO83_CORR.indel.NC_017659.1.fake.1.4.1700.6000.mapping.gff >out2.pO83_CORR.indel.out2.reads_mapping.gff;rm out2.pO83_CORR.indel.NC_017659.1.fake.1.4.long_reads.ylabel.gff out2.pO83_CORR.indel.NC_017659.1.fake.1.4.1700.6000.mapping.gff;echo output out2.pO83_CORR.indel.out2.reads_mapping.gff
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set -vex;cat out2.pO83_CORR.indel.NC_017659.1.fake.1.4.long_reads.ylabel.setting.conf out2.pO83_CORR.indel.NC_017659.1.fake.1.4.1700.6000.mapping.setting.conf > out2.pO83_CORR.indel.out2.reads_mapping.setting.conf;rm out2.pO83_CORR.indel.NC_017659.1.fake.1.4.long_reads.ylabel.setting.conf out2.pO83_CORR.indel.NC_017659.1.fake.1.4.1700.6000.mapping.setting.conf;echo output out2.pO83_CORR.indel.out2.reads_mapping.setting.conf
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set -vex;cat out2.pO83_CORR.out2.reads_mapping.crosslink >out2.reads_mapping.crosslink
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set -vex;cat out2.pO83_CORR.out2.reads_mapping.setting.conf >out2.reads_mapping.setting.conf
20+
set -vex;cat out2.pO83_CORR.out2.reads_mapping.setting.conf out2.pO83_CORR.indel.out2.reads_mapping.setting.conf >out2.reads_mapping.setting.conf
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set -vex;cat pO83_CORR.pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.gff >out2.pO83_CORR.out2.synteny.gff;rm pO83_CORR.pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.gff;echo output out2.pO83_CORR.out2.synteny.gff
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set -vex;cat pO83_CORR.pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.setting.conf > out2.pO83_CORR.out2.synteny.setting.conf;rm pO83_CORR.pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.setting.conf;echo output out2.pO83_CORR.out2.synteny.setting.conf
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set -vex;cat out2.pO83_CORR.indel.pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.gff >out2.pO83_CORR.indel.out2.synteny.gff;rm out2.pO83_CORR.indel.pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.gff;echo output out2.pO83_CORR.indel.out2.synteny.gff
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set -vex;cat out2.pO83_CORR.indel.pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.setting.conf > out2.pO83_CORR.indel.out2.synteny.setting.conf;rm out2.pO83_CORR.indel.pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.setting.conf;echo output out2.pO83_CORR.indel.out2.synteny.setting.conf
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set -vex;cat pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.crosslink.conf >out2.pO83_CORR.indel.to.pO83_CORR.out2.synteny.crosslink;rm pO83_CORR.indel.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.crosslink.conf;echo output out2.pO83_CORR.indel.to.pO83_CORR.out2.synteny.crosslink
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set -vex;cat out2.pO83_CORR.indel.to.pO83_CORR.out2.synteny.crosslink >out2.synteny.crosslink
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set -vex;cat out2.pO83_CORR.out2.synteny.setting.conf out2.pO83_CORR.indel.out2.synteny.setting.conf >out2.synteny.setting.conf
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set -vex;cat out2.reads_mapping.setting.conf out2.synteny.setting.conf >feature.color.label.conf.out2
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set -vex;cat out2.reads_mapping.setting.conf >feature.color.label.conf.out2
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set -vex;cat out2.reads_mapping.crosslink out2.synteny.crosslink >feature.crossing.link.out2
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set -vex;cat out2.reads_mapping.crosslink >feature.crossing.link.out2
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set -vex;cat out2.pO83_CORR.out2.reads_mapping.gff out2.pO83_CORR.indel.out2.reads_mapping.gff out2.pO83_CORR.out2.synteny.gff out2.pO83_CORR.indel.out2.synteny.gff|awk -F '{print }'|sort -u
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set -vex;cat out2.pO83_CORR.out2.reads_mapping.gff|awk -F '{print }'|sort -u
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set -vex;sed -r 's/^(pO83_CORR\s.*\.gff)\s/\1,out2.pO83_CORR.out2.reads_mapping.gff,out2.pO83_CORR.out2.synteny.gff\t/' tracks.2.list >tracks.2.list.out2;cp tracks.2.list.out2 tracks.2.list.out2.tmp
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set -vex;sed -r 's/^(pO83_CORR\s.*\.gff)\s/\1,out2.pO83_CORR.out2.reads_mapping.gff\t/' tracks.2.list >tracks.2.list.out2;cp tracks.2.list.out2 tracks.2.list.out2.tmp
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set -vex;sed -r 's/^(pO83_CORR.indel\s.*\.gff)\s/\1,out2.pO83_CORR.indel.out2.reads_mapping.gff,out2.pO83_CORR.indel.out2.synteny.gff\t/' tracks.2.list.out2.tmp >tracks.2.list.out2;cp tracks.2.list.out2 tracks.2.list.out2.tmp
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