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update
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[email protected] committed Dec 23, 2018
1 parent 02aae96 commit e3f5419
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Showing 72 changed files with 465,620 additions and 19,335 deletions.
9,607 changes: 9,607 additions & 0 deletions data/s4.seq.sam.sorted.bam.s4000.1.9609.depth
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252 changes: 195 additions & 57 deletions example/chr14.14.1.1.66901400.66903400.mapping.setting.conf
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290 changes: 199 additions & 91 deletions example/chr14.14.1.2.66901400.66903400.depth.setting.conf
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529 changes: 291 additions & 238 deletions example/chr14.14.1.2.66901400.66903400.mapping.setting.conf
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476 changes: 238 additions & 238 deletions example/chr14.14.1.3.66901400.66903400.mapping.setting.conf
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368 changes: 184 additions & 184 deletions example/chr14.14.1.4.66901400.66903400.mapping.setting.conf
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4 changes: 2 additions & 2 deletions example/chr14.14.1.5.66901400.66903400.mapping.setting.conf
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Expand Up @@ -13,7 +13,7 @@ chr14.14.vcf.66901580.C.to.T.rs1350330.5 pos_feature_label medium_up
chr14.14.vcf.66901580.C.to.T.rs1350330.5 feature_label_auto_angle_flag 0
chr14.14.vcf.66901580.C.to.T.rs1350330.5 label_rotate_angle -15
chr14.14.vcf.66901580.C.to.T.rs1350330.5 feature_label_size 2
chr14.14.vcf.66901580.C.to.T.rs1350330.5 feature_x_extent -2bp,+2bp
chr14.14.vcf.66901580.C.to.T.rs1350330.5 feature_popup_title mutation: 14:66901580:rs1350330: C -> T;qual=50,PASS platforms=4;platformnames=Illumina,CG,10X,Solid;datasets=6;datasetnames=HiSeqPE300x,CGnormal,HiSeq250x250,10XChromium,HiSeqMatePair,SolidSE75bp;callsets=9;callsetnames=HiSeqPE300xGATK,CGnormal,HiSeqPE300xfreebayes,HiSeq250x250GATK,HiSeq250x250freebayes,10XGATKhaplo,HiSeqMatePairGATK,HiSeqMatePairfreebayes,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable,CS_HiSeq250x250GATK_callable GT:DP:ADALL:AD:GQ:IGT:IPS:PS 1|0:1095:214,210:251,267:1323:0/1:.:PATMAT
chr14.14.vcf.66903247.A.to.G.rs933039.5 feature_color Purple
chr14.14.vcf.66903247.A.to.G.rs933039.5 feature_label_color Purple
chr14.14.vcf.66903247.A.to.G.rs933039.5 feature_shape rect
Expand All @@ -29,4 +29,4 @@ chr14.14.vcf.66903247.A.to.G.rs933039.5 pos_feature_label medium_up
chr14.14.vcf.66903247.A.to.G.rs933039.5 feature_label_auto_angle_flag 0
chr14.14.vcf.66903247.A.to.G.rs933039.5 label_rotate_angle -15
chr14.14.vcf.66903247.A.to.G.rs933039.5 feature_label_size 2
chr14.14.vcf.66903247.A.to.G.rs933039.5 feature_x_extent -2bp,+2bp
chr14.14.vcf.66903247.A.to.G.rs933039.5 feature_popup_title mutation: 14:66903247:rs933039: A -> G;qual=50,PASS platforms=4;platformnames=Illumina,CG,10X,Solid;datasets=6;datasetnames=HiSeqPE300x,CGnormal,HiSeq250x250,10XChromium,HiSeqMatePair,SolidSE75bp;callsets=9;callsetnames=HiSeqPE300xGATK,CGnormal,HiSeqPE300xfreebayes,HiSeq250x250GATK,HiSeq250x250freebayes,10XGATKhaplo,HiSeqMatePairGATK,HiSeqMatePairfreebayes,SolidSE75GATKHC;datasetsmissingcall=IonExome;callable=CS_HiSeqPE300xGATK_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable,CS_HiSeq250x250GATK_callable GT:DP:ADALL:AD:GQ:IGT:IPS:PS 1|0:1059:206,182:248,242:1139:0/1:.:PATMAT
290 changes: 199 additions & 91 deletions example/chr14.hist_scatter_line.setting.conf
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474 changes: 237 additions & 237 deletions example/chr14.read_mapping.crosslink
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1,629 changes: 910 additions & 719 deletions example/chr14.read_mapping.setting.conf
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2,532 changes: 1,679 additions & 853 deletions example/feature.color.label.conf10.new
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1,919 changes: 1,109 additions & 810 deletions example/feature.color.label.conf11.new
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74,004 changes: 74,004 additions & 0 deletions example/feature.color.label.conf7
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474 changes: 237 additions & 237 deletions example/feature.crossing.link.conf11
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2 changes: 1 addition & 1 deletion example/list7.new
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@@ -1,4 +1,4 @@
s1 s1.gff,s1.synteny.gff s1.seq
s2 s2.gff,s2.synteny.gff s2.seq
s3 s3.gff,s3.synteny.gff s3.seq
s4 s4.gff,s4.synteny.gff s4.seq
s4 s4.gff,s4.synteny.gff,s4.read_mapping.gff,s4.hist_scatter_line.gff s4.seq
11 changes: 7 additions & 4 deletions example/main.7.conf
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Expand Up @@ -3,7 +3,7 @@ svg_width_height = 1200,600 # *
pdf_dpi = 100

# plot feature type
feature_keywords = gene,synteny,xxxxx # *
feature_keywords = gene,synteny,short_reads,hist_scatter_line,xxxxx # *
feature_setting = feature.color.label.conf7 # *

# figure width layout
Expand Down Expand Up @@ -101,11 +101,14 @@ scale_tick_padding_y=15
scale_tick_fontsize=13


synteny = order->1,query->s1:target->s2,../data/s1.mapto.s2.paf.gz,paf,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.5,cross_link_shift_y->+3:-3
#synteny = order->1,query->s1:target->s2,../data/s1.mapto.s2.paf.gz,paf,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.5,cross_link_shift_y->+3:-3

#synteny = order->1,query->s2:target->s3,../data/s2.mapto.s3.paf.gz,paf,quadrilateral,forward->yellow->opacity1,reverse->blue->opacity1
synteny = order->0,query->s2:target->s4,../data/s2.mapto.s4.paf.gz,paf,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3

#reads_mapping=short_reads,1,s4,s4000,0,../data/s4.seq.sam.sorted.bam:../data/s4.seq,rainbow:color->blue:opacity->0.5:cross_link_width_ellipse->0.05,-55->-100,0,10->40->3,ytick_label_text,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 ylabel->illuminate read mapping,gap:150bp,fontsize:10,color:green
#synteny = order->0,query->s2:target->s4,../data/s2.mapto.s4.paf.gz,paf,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3

hist_scatter_line = hist,0,s4,s4000,0,50,../data/s4.seq.sam.sorted.bam:../data/s4.seq,color->green:opacity->1,-55->-100,ytick_flag,1->100->10,ytick_label_text,hgrid_flag,green:green,0.6:0.3,0.6:0.6:0.2:0.2,5:5 ylabel->illuminate read depth,gap:150bp,fontsize:13,color:black
reads_mapping=short_reads,1,s4,s4000,0,../data/s4.seq.sam.sorted.bam:../data/s4.seq,stack,-5->-50,0,10->40->3,ytick_label_text,0,green:black,1:1,2:6:0.2:0.1,15:15,0:10:40 ylabel->illuminate read mapping,gap:150bp,fontsize:10,color:green

#reads_mapping=long_reads,1,s4,s4000,0,../data/s4.seq.longreads.map2ref.sort.bam:../data/s4.seq,stack,-10->-50,0,20->30->2,ytick_label_text,0,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:height0:0bp:rect ylabel->pacbio read mapping,gap:150bp,fontsize:13,color:black

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