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fix bug
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[email protected] committed Nov 12, 2019
1 parent a4e4a09 commit 7ef967b
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Showing 19 changed files with 74,661 additions and 74,645 deletions.
29,614 changes: 14,807 additions & 14,807 deletions example/feature.color.label.conf.out2
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2,738 changes: 1,369 additions & 1,369 deletions example/feature.crossing.link.out2
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14 changes: 7 additions & 7 deletions example/main.2.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ chr_id=NC_017659.1
data_file=../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam:../data/NC_017659.1.fa
ylabel=illuminate pair-end read mapping,gap:50bp,fontsize:13,color:black
data_display_shape=rainbow:color->blue:opacity->0.8:cross_link_width_ellipse->0.05
#subtrack_yaxis_bg_region=5->33
subtrack_yaxis_bg_region=5->33
#skip = 1
}

Expand All @@ -20,7 +20,7 @@ chr_id = NC_017659.1
data_file = ../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam:../data/NC_017659.1.fa
data_display_shape = stack
ylabel = illuminate pair-end read mapping stack,gap:50bp,fontsize:13,color:black
#subtrack_yaxis_bg_region=35->65
subtrack_yaxis_bg_region=35->65
#skip = 1
}

Expand All @@ -32,7 +32,7 @@ chr_id = NC_017659.1
data_file = ../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.longreads.sort.bam:../data/NC_017659.1.fa
data_display_shape = stack
ylabel = pacbio read mapping stack,gap:50bp,fontsize:13,color:black
#subtrack_yaxis_bg_region = 70->100
subtrack_yaxis_bg_region = 70->100
#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:height0.9:5bp:rect,H:blue:opacity0.6:height0.2:5bp: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
#chop_soft_clip = no
#skip = 1
Expand All @@ -46,7 +46,7 @@ chr_id = NC_017659.1
data_file = ../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam:../data/NC_017659.1.fa
data_display_shape = rainbow:color->blue:opacity->0.8:cross_link_width_ellipse->0.05
ylabel = illuminate pair-end read mapping,gap:50bp,fontsize:13,color:black
#subtrack_yaxis_bg_region = 5->33
subtrack_yaxis_bg_region = 5->33
#skip = 1
}

Expand All @@ -57,7 +57,7 @@ chr_id = NC_017659.1
data_file = ../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam:../data/NC_017659.1.fa
data_display_shape = stack
ylabel = illuminate pair-end read mapping stack,gap:50bp,fontsize:13,color:black
#subtrack_yaxis_bg_region = 35->65
subtrack_yaxis_bg_region = 35->65
#skip = 1
}

Expand All @@ -68,7 +68,7 @@ chr_id = NC_017659.1
data_file = ../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.longreads.sort.bam:../data/NC_017659.1.fa
data_display_shape = stack
ylabel = pacbio read mapping stack,gap:50bp,fontsize:13,color:black
#subtrack_yaxis_bg_region = 70->95
subtrack_yaxis_bg_region = 70->95
#skip = 1
}

Expand All @@ -81,7 +81,7 @@ chr_id = NC_017659.1.fake
data_file = ../data/NC_017659.1.indel.fa.longreads.map2ref.sort.bam:../data/NC_017659.1.indel.fa
data_display_shape = stack
ylabel = pacbio read mapping stack,gap:50bp,fontsize:13,color:black
#subtrack_yaxis_bg_region = -20->-100
subtrack_yaxis_bg_region = -20->-100
#skip = 1
}

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14 changes: 7 additions & 7 deletions example/main.2.conf.out2
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Original file line number Diff line number Diff line change
Expand Up @@ -85,13 +85,13 @@ cross_link_order = 2
label_text_anchor = middle
pdf_dpi = 100

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,rainbow:color->blue:opacity->0.8:cross_link_width_ellipse->0.05,86.8571428571429->100,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->illuminate pair-end read mapping,gap:50bp,fontsize:13,color:black
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,72.7142857142857->85.8571428571429,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->illuminate pair-end read mapping stack,gap:50bp,fontsize:13,color:black
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,58.5714285714286->71.7142857142857,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
reads_mapping = short_reads,1,pO83_CORR.twin,NC_017659.1,0,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam:../data/NC_017659.1.fa,rainbow:color->blue:opacity->0.8:cross_link_width_ellipse->0.05,44.4285714285714->57.5714285714286,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->illuminate pair-end read mapping,gap:50bp,fontsize:13,color:black
reads_mapping = short_reads,1,pO83_CORR.twin,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,30.2857142857143->43.4285714285714,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->illuminate pair-end read mapping stack,gap:50bp,fontsize:13,color:black
reads_mapping = long_reads,1,pO83_CORR.twin,NC_017659.1,0,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.longreads.sort.bam:../data/NC_017659.1.fa,stack,16.1428571428572->29.2857142857143,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
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,2.00000000000002->15.1428571428572,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
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,rainbow:color->blue:opacity->0.8:cross_link_width_ellipse->0.05,5->33,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->illuminate pair-end read mapping,gap:50bp,fontsize:13,color:black
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->65,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->illuminate pair-end read mapping stack,gap:50bp,fontsize:13,color:black
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->100,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
reads_mapping = short_reads,1,pO83_CORR.twin,NC_017659.1,0,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.sr.sam.sorted.bam:../data/NC_017659.1.fa,rainbow:color->blue:opacity->0.8:cross_link_width_ellipse->0.05,5->33,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->illuminate pair-end read mapping,gap:50bp,fontsize:13,color:black
reads_mapping = short_reads,1,pO83_CORR.twin,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->65,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->illuminate pair-end read mapping stack,gap:50bp,fontsize:13,color:black
reads_mapping = long_reads,1,pO83_CORR.twin,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->95,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black
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->-100,0,1->100->10,ytick_label,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 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:height0.9:5bp: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,read1:green:opacity0.6:height0.8:6bp:arrow,read2:#1E90FF:opacity0.6:height0.8:1bp:arrow,fake:white:opacity1:height0.8:0bp:rect,diploid:red:opacity0.8:height0.5:1bp:rect; ylabel->pacbio read mapping stack,gap:50bp,fontsize:13,color:black

chop_soft_clip = yes
label_text_alignment_baseline = baseline
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